List all resources, or create a new resource.

GET /api/t/?topicID=%22topic_3510%22
HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept

{
    "count": 256,
    "next": "?page=2",
    "previous": null,
    "list": [
        {
            "name": "ProtVar",
            "description": "ProtVar helps users to contextualise and evaluate human missense variation at a per-residue level. It can be accessed via genomic coordinates, IDs or protein positions in over 92% of human proteins. Functional and structural annotations, predictions and co-located variants can be explored via an interactive UI or accessed programatically via an API.",
            "homepage": "https://www.ebi.ac.uk/ProtVar/",
            "biotoolsID": "protvar",
            "biotoolsCURIE": "biotools:protvar",
            "version": [],
            "otherID": [],
            "relation": [
                {
                    "biotoolsID": "open_targets_platform",
                    "type": "usedBy"
                },
                {
                    "biotoolsID": "uniprot",
                    "type": "uses"
                },
                {
                    "biotoolsID": "uniprot",
                    "type": "usedBy"
                },
                {
                    "biotoolsID": "ensembl",
                    "type": "uses"
                },
                {
                    "biotoolsID": "pdbe",
                    "type": "uses"
                },
                {
                    "biotoolsID": "dbsnp",
                    "type": "uses"
                },
                {
                    "biotoolsID": "clinvar",
                    "type": "uses"
                },
                {
                    "biotoolsID": "crossmap",
                    "type": "uses"
                },
                {
                    "biotoolsID": "alphafold_2",
                    "type": "uses"
                },
                {
                    "biotoolsID": "eve",
                    "type": "uses"
                },
                {
                    "biotoolsID": "cadd_phred",
                    "type": "uses"
                }
            ],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2520",
                            "term": "DNA mapping"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2887",
                                "term": "Nucleic acid sequence record"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3016",
                                    "term": "VCF"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2886",
                                "term": "Protein sequence record"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_2187",
                                    "term": "UniProt-like (text)"
                                }
                            ]
                        }
                    ],
                    "note": "ProtVar maps missense variants from genomic coordinates to UniProt protein positions in all isoforms.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_3661",
                            "term": "SNP annotation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2887",
                                "term": "Nucleic acid sequence record"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3016",
                                    "term": "VCF"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_3779",
                                "term": "Annotated text"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_2187",
                                    "term": "UniProt-like (text)"
                                }
                            ]
                        }
                    ],
                    "note": "ProtVar annotates missense variant positions with functional and structural information for the amino acid affected, the protein region and the overall protein role from curated and high throughput sources.",
                    "cmd": null
                }
            ],
            "toolType": [
                "Web application",
                "Web API",
                "Bioinformatics portal"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0091",
                    "term": "Bioinformatics"
                },
                {
                    "uri": "http://edamontology.org/topic_3574",
                    "term": "Human genetics"
                },
                {
                    "uri": "http://edamontology.org/topic_1317",
                    "term": "Structural biology"
                },
                {
                    "uri": "http://edamontology.org/topic_2533",
                    "term": "DNA mutation"
                },
                {
                    "uri": "http://edamontology.org/topic_3510",
                    "term": "Protein sites, features and motifs"
                }
            ],
            "operatingSystem": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "language": [
                "Java"
            ],
            "license": null,
            "collectionID": [
                "Rare Disease"
            ],
            "maturity": "Mature",
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://twitter.com/EBIProtVar",
                    "type": [
                        "Social media"
                    ],
                    "note": null
                },
                {
                    "url": "https://docs.google.com/forms/d/e/1FAIpQLSd7P85zRHVspesU3kgF3qWpzSDSYFsyeGFmnkuyzB00HNDmDw/viewform?usp=sf_link",
                    "type": [
                        "Mailing list"
                    ],
                    "note": null
                }
            ],
            "download": [],
            "documentation": [
                {
                    "url": "https://www.ebi.ac.uk/ProtVar/help",
                    "type": [
                        "User manual"
                    ],
                    "note": "This is a link to the help section in ProtVar with annotated screen shots to help you navigate the tool and understand the data."
                }
            ],
            "publication": [],
            "credit": [
                {
                    "name": "James Stephenson",
                    "email": "jstephenson@ebi.ac.uk",
                    "url": "https://www.ebi.ac.uk/people/person/james-stephenson/",
                    "orcidid": "https://orcid.org/0000-0002-6427-5703",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Primary contact",
                        "Maintainer",
                        "Documentor"
                    ],
                    "note": null
                },
                {
                    "name": "EMBL-EBI",
                    "email": null,
                    "url": "https://www.ebi.ac.uk/",
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Institute",
                    "typeRole": [
                        "Provider"
                    ],
                    "note": null
                },
                {
                    "name": "Prabhat Totoo",
                    "email": null,
                    "url": "https://www.ebi.ac.uk/people/person/prabhat-totoo/",
                    "orcidid": "https://orcid.org/0000-0001-5923-4467",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Developer",
                        "Maintainer"
                    ],
                    "note": null
                },
                {
                    "name": "Open Targets",
                    "email": null,
                    "url": "https://www.opentargets.org/",
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Consortium",
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "JStephenson",
            "additionDate": "2023-09-21T09:05:33.125111Z",
            "lastUpdate": "2023-09-25T09:31:39.599149Z",
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": null
        },
        {
            "name": "ProFeatMap",
            "description": "Python based program creating highly customizable 2D maps showing elements of interests (domains, repeats, PTM sites,...) called feature as defined in Uniprot.",
            "homepage": "https://profeatmap.pythonanywhere.com/",
            "biotoolsID": "profeatmap",
            "biotoolsCURIE": "biotools:profeatmap",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_3937",
                            "term": "Feature extraction"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0239",
                            "term": "Sequence motif recognition"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0417",
                            "term": "PTM site prediction"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Web application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0601",
                    "term": "Protein modifications"
                },
                {
                    "uri": "http://edamontology.org/topic_0102",
                    "term": "Mapping"
                },
                {
                    "uri": "http://edamontology.org/topic_3510",
                    "term": "Protein sites, features and motifs"
                },
                {
                    "uri": "http://edamontology.org/topic_3293",
                    "term": "Phylogenetics"
                }
            ],
            "operatingSystem": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "language": [
                "Python"
            ],
            "license": "GPL-3.0",
            "collectionID": [],
            "maturity": null,
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://github.com/profeatmap/ProFeatMap",
                    "type": [
                        "Repository"
                    ],
                    "note": null
                }
            ],
            "download": [],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.1093/BIOADV/VBAD022",
                    "pmid": "36936371",
                    "pmcid": "PMC10023195",
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "ProFeatMap: a highly customizable tool for 2D feature representation of protein sets",
                        "abstract": "Motivation: Studies of sets of proteins are a central point in biology. In particular, the application of omics in the last decades has generated lists of several hundreds or thousands of proteins or genes. However, these lists are often not inspected globally, possibly due to the lack of tools capable of simultaneously visualizing the feature architectures of a large number of proteins. Results: Here, we present ProFeatMap, an intuitive Python-based website. For a given set of proteins, it allows to display features such as domains, repeats, disorder or post-translational modifications and their organization along the sequences, into a highly customizable 2D map. Starting from a user-defined protein list of UniProt accession codes, ProFeatMap extracts the most important annotated features available for each protein from one of the wellestablished databases such as Uniprot or InterPro, allocates shapes and colors, potentially depending on quantitative or qualitative data and sorts the protein list based on homologous feature content. The resulting publicationquality map allows even large protein families to be explored, and to classify them based on shared features. It can help to gain insights, for example, feature redundancy or feature pattern, that were previously overlooked. ProFeatMap is freely available on the web at: https://profeatmap.pythonanywhere.com/. Availability and implementation: Source code is freely accessible at https://github.com/profeatmap/ProFeatMap under the GPL license.",
                        "date": "2023-01-01T00:00:00Z",
                        "citationCount": 0,
                        "authors": [
                            {
                                "name": "Bich G."
                            },
                            {
                                "name": "Monsellier E."
                            },
                            {
                                "name": "Trave G."
                            },
                            {
                                "name": "Nomine Y."
                            }
                        ],
                        "journal": "Bioinformatics Advances"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Goran Bich",
                    "email": "goran.bich@igbmc.fr",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Yves Nominé",
                    "email": "yves.nomine@igbmc.fr",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-2912-116X",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "Pub2Tools",
            "additionDate": "2023-09-15T15:49:57.043304Z",
            "lastUpdate": "2023-09-15T15:49:57.045986Z",
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        },
        {
            "name": "BioExcel Building Blocks tutorials: Protein Conformational Transitions",
            "description": "This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks (biobb).",
            "homepage": "https://mmb.irbbarcelona.org/biobb/workflows/tutorials/godmd",
            "biotoolsID": "bioexcel_building_blocks_tutorials_protein_conformational_transitions",
            "biotoolsCURIE": "biotools:bioexcel_building_blocks_tutorials_protein_conformational_transitions",
            "version": [
                "1.0"
            ],
            "otherID": [],
            "relation": [
                {
                    "biotoolsID": "biobb",
                    "type": "uses"
                },
                {
                    "biotoolsID": "godmd",
                    "type": "uses"
                },
                {
                    "biotoolsID": "water",
                    "type": "uses"
                }
            ],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0477",
                            "term": "Protein modelling"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2476",
                            "term": "Molecular dynamics"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2480",
                            "term": "Structure analysis"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0570",
                            "term": "Structure visualisation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3890",
                            "term": "Trajectory visualization"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_3870",
                                "term": "Trajectory data"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3878",
                                    "term": "mdcrd"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3874",
                                    "term": "PCAzip"
                                }
                            ]
                        }
                    ],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Workflow"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_2814",
                    "term": "Protein structure analysis"
                },
                {
                    "uri": "http://edamontology.org/topic_3892",
                    "term": "Biomolecular simulation"
                },
                {
                    "uri": "http://edamontology.org/topic_3510",
                    "term": "Protein sites, features and motifs"
                },
                {
                    "uri": "http://edamontology.org/topic_2275",
                    "term": "Molecular modelling"
                },
                {
                    "uri": "http://edamontology.org/topic_2814",
                    "term": "Protein structure analysis"
                },
                {
                    "uri": "http://edamontology.org/topic_0092",
                    "term": "Data visualisation"
                }
            ],
            "operatingSystem": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "language": [
                "Python"
            ],
            "license": "Apache-2.0",
            "collectionID": [
                "BioExcel"
            ],
            "maturity": "Emerging",
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [
                "Tools",
                "Interoperability"
            ],
            "elixirNode": [
                "Spain",
                "UK"
            ],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://mmb.irbbarcelona.org/biobb/workflows/tutorials/godmd",
                    "type": [
                        "Other"
                    ],
                    "note": "Tutorial in HTML"
                },
                {
                    "url": "https://biobb-wf-godmd.readthedocs.io/en/latest/index.html",
                    "type": [
                        "Other"
                    ],
                    "note": "Tutorial in Read the Docs"
                },
                {
                    "url": "https://github.com/bioexcel/biobb_wf_godmd",
                    "type": [
                        "Repository"
                    ],
                    "note": "Source Code in GitHub"
                }
            ],
            "download": [
                {
                    "url": "https://github.com/bioexcel/biobb_wf_godmd",
                    "type": "Source code",
                    "note": "Source Code in GitHub",
                    "version": "1.0"
                },
                {
                    "url": "https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_godmd/main?filepath=biobb_wf_godmd%2Fnotebooks%2Fbiobb_wf_godmd.ipynb",
                    "type": "VM image",
                    "note": "BioExcel Binder",
                    "version": null
                }
            ],
            "documentation": [
                {
                    "url": "https://biobb-wf-godmd.readthedocs.io/en/latest/index.html",
                    "type": [
                        "Other"
                    ],
                    "note": "Documentation in Read the Docs"
                }
            ],
            "publication": [
                {
                    "doi": "10.1038/s41597-019-0177-4",
                    "pmid": "31506435",
                    "pmcid": "PMC6736963",
                    "type": [
                        "Other"
                    ],
                    "version": null,
                    "note": "BioExcel Building Blocks (BioBB)",
                    "metadata": {
                        "title": "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows",
                        "abstract": "In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments.",
                        "date": "2019-12-01T00:00:00Z",
                        "citationCount": 33,
                        "authors": [
                            {
                                "name": "Andrio P."
                            },
                            {
                                "name": "Hospital A."
                            },
                            {
                                "name": "Conejero J."
                            },
                            {
                                "name": "Jorda L."
                            },
                            {
                                "name": "Del Pino M."
                            },
                            {
                                "name": "Codo L."
                            },
                            {
                                "name": "Soiland-Reyes S."
                            },
                            {
                                "name": "Goble C."
                            },
                            {
                                "name": "Lezzi D."
                            },
                            {
                                "name": "Badia R.M."
                            },
                            {
                                "name": "Orozco M."
                            },
                            {
                                "name": "Gelpi J.L."
                            }
                        ],
                        "journal": "Scientific Data"
                    }
                },
                {
                    "doi": "10.1093/bioinformatics/btt324",
                    "pmid": "23740746",
                    "pmcid": null,
                    "type": [
                        "Other"
                    ],
                    "version": null,
                    "note": "GOdMD method",
                    "metadata": {
                        "title": "Exploration of conformational transition pathways from coarse-grained simulations",
                        "abstract": "Motivation: A new algorithm to trace conformational transitions in proteins is presented. The method uses discrete molecular dynamics as engine to sample protein conformational space. A multiple minima Go-like potential energy function is used in combination with several enhancing sampling strategies, such as metadynamics, Maxwell Demon molecular dynamics and essential dynamics. The method, which shows an unprecedented computational efficiency, is able to trace a wide range of known experimental transitions. Contrary to simpler methods our strategy does not introduce distortions in the chemical structure of the protein and is able to reproduce well complex non-linear conformational transitions. The method, called GOdMD, can easily introduce additional restraints to the transition (presence of ligand, known intermediate, known maintained contacts, ...) and is freely distributed to the community through the Spanish National Bioinformatics Institute (http://mmb.irbbarcelona.org/GOdMD).Availability: Freely available on the web at http://mmb.irbbarcelona.org/GOdMD.Contact: or modesto@mmb.pcb.ub.esSupplementary information: Supplementary data are available at Bioinformatics online. © 2013 The Author 2013. Published by Oxford University Press.",
                        "date": "2013-08-15T00:00:00Z",
                        "citationCount": 24,
                        "authors": [
                            {
                                "name": "Sfriso P."
                            },
                            {
                                "name": "Hospital A."
                            },
                            {
                                "name": "Emperador A."
                            },
                            {
                                "name": "Orozco M."
                            }
                        ],
                        "journal": "Bioinformatics"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Adam Hospital Gasch",
                    "email": "adam.hospital@irbbarcelona.org",
                    "url": "https://www.irbbarcelona.org/en/research/adam-hospital",
                    "orcidid": "https://orcid.org/0000-0002-8291-8071",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Primary contact",
                        "Developer",
                        "Documentor",
                        "Maintainer"
                    ],
                    "note": null
                },
                {
                    "name": "Genís Bayarri",
                    "email": "genis.bayarri@irbbarcelona.org",
                    "url": "https://www.irbbarcelona.org/es/research/genis-bayarri",
                    "orcidid": "https://orcid.org/0000-0003-0513-0288",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Contributor",
                        "Developer",
                        "Maintainer"
                    ],
                    "note": null
                },
                {
                    "name": "BioExcel CoE",
                    "email": null,
                    "url": "https://bioexcel.eu/",
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Consortium",
                    "typeRole": [
                        "Provider"
                    ],
                    "note": null
                }
            ],
            "community": null,
            "owner": "adam.hospital@irbbarcelona.org",
            "additionDate": "2023-08-31T07:04:02.274853Z",
            "lastUpdate": "2023-08-31T07:33:54.784700Z",
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": null
        },
        {
            "name": "IPs-GRUAtt",
            "description": "An attention-based bidirectional gated recurrent unit network for predicting phosphorylation sites of SARS-CoV-2 infection.",
            "homepage": "http://cbcb.cdutcm.edu.cn/phosphory/",
            "biotoolsID": "ips-gruatt",
            "biotoolsCURIE": "biotools:ips-gruatt",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0417",
                            "term": "PTM site prediction"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3927",
                            "term": "Network analysis"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0477",
                            "term": "Protein modelling"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1233",
                                "term": "Sequence set (protein)"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_2182",
                                    "term": "FASTQ-like format (text)"
                                }
                            ]
                        }
                    ],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Web application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0601",
                    "term": "Protein modifications"
                },
                {
                    "uri": "http://edamontology.org/topic_3474",
                    "term": "Machine learning"
                },
                {
                    "uri": "http://edamontology.org/topic_3510",
                    "term": "Protein sites, features and motifs"
                },
                {
                    "uri": "http://edamontology.org/topic_0602",
                    "term": "Molecular interactions, pathways and networks"
                }
            ],
            "operatingSystem": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "language": [],
            "license": null,
            "collectionID": [
                "COVID-19"
            ],
            "maturity": null,
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://github.com/GreatChenLab/IPs-GRUAtt",
                    "type": [
                        "Repository"
                    ],
                    "note": null
                }
            ],
            "download": [],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.1016/J.OMTN.2023.02.027",
                    "pmid": "36908648",
                    "pmcid": "PMC9968446",
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "IPs-GRUAtt: An attention-based bidirectional gated recurrent unit network for predicting phosphorylation sites of SARS-CoV-2 infection",
                        "abstract": "The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has generated tremendous concern and poses a serious threat to international public health. Phosphorylation is a common post-translational modification affecting many essential cellular processes and is inextricably linked to SARS-CoV-2 infection. Hence, accurate identification of phosphorylation sites will be helpful to understand the mechanisms of SARS-CoV-2 infection and mitigate the ongoing COVID-19 pandemic. In the present study, an attention-based bidirectional gated recurrent unit network, called IPs-GRUAtt, was proposed to identify phosphorylation sites in SARS-CoV-2-infected host cells. Comparative results demonstrated that IPs-GRUAtt surpassed both state-of-the-art machine-learning methods and existing models for identifying phosphorylation sites. Moreover, the attention mechanism made IPs-GRUAtt able to extract the key features from protein sequences. These results demonstrated that the IPs-GRUAtt is a powerful tool for identifying phosphorylation sites. For facilitating its academic use, a freely available online web server for IPs-GRUAtt is provided at http://cbcb.cdutcm.edu.cn/phosphory/.",
                        "date": "2023-06-13T00:00:00Z",
                        "citationCount": 0,
                        "authors": [
                            {
                                "name": "Zhang G."
                            },
                            {
                                "name": "Tang Q."
                            },
                            {
                                "name": "Feng P."
                            },
                            {
                                "name": "Chen W."
                            }
                        ],
                        "journal": "Molecular Therapy - Nucleic Acids"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Pengmian Feng",
                    "email": "fengpengmian@gmail.com",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Wei Chen",
                    "email": "greatchen@ncst.edu.cn",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Guiyang Zhang",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Qiang Tang",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "Pub2Tools",
            "additionDate": "2023-08-24T08:12:53.062600Z",
            "lastUpdate": "2023-08-24T08:12:53.065780Z",
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        },
        {
            "name": "3D-BioInfo + BioExcel: Protein Conformational Ensembles Generation",
            "description": "This workflow illustrates the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb). Workflow included in the ELIXIR 3D-Bioinfo Implementation Study: Building on PDBe-KB to chart and characterize the conformation landscape of native proteins",
            "homepage": "https://mmb.irbbarcelona.org/biobb/workflows#protein-conformational-ensembles-generation",
            "biotoolsID": "3d-bioinfo_bioexcel_protein_conformational_ensembles_generation",
            "biotoolsCURIE": "biotools:3d-bioinfo_bioexcel_protein_conformational_ensembles_generation",
            "version": [
                "1.0"
            ],
            "otherID": [],
            "relation": [
                {
                    "biotoolsID": "biobb",
                    "type": "uses"
                },
                {
                    "biotoolsID": "imod",
                    "type": "uses"
                },
                {
                    "biotoolsID": "flexserv",
                    "type": "uses"
                },
                {
                    "biotoolsID": "prody",
                    "type": "uses"
                },
                {
                    "biotoolsID": "nglview",
                    "type": "uses"
                }
            ],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0474",
                            "term": "Protein structure prediction"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2406",
                            "term": "Protein structure analysis"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3891",
                            "term": "Essential dynamics"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3890",
                            "term": "Trajectory visualization"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0250",
                            "term": "Protein property calculation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2939",
                            "term": "Principal component visualisation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_3870",
                                "term": "Trajectory data"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3464",
                                    "term": "JSON"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3874",
                                    "term": "PCAzip"
                                }
                            ]
                        }
                    ],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Workflow"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_3892",
                    "term": "Biomolecular simulation"
                },
                {
                    "uri": "http://edamontology.org/topic_0081",
                    "term": "Structure analysis"
                },
                {
                    "uri": "http://edamontology.org/topic_3510",
                    "term": "Protein sites, features and motifs"
                },
                {
                    "uri": "http://edamontology.org/topic_0082",
                    "term": "Structure prediction"
                },
                {
                    "uri": "http://edamontology.org/topic_0092",
                    "term": "Data visualisation"
                }
            ],
            "operatingSystem": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "language": [
                "Python"
            ],
            "license": "Apache-2.0",
            "collectionID": [
                "BioExcel",
                "3D-BioInfo",
                "3D-BioInfo-Protein-Complex"
            ],
            "maturity": "Emerging",
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [
                "Interoperability",
                "Tools"
            ],
            "elixirNode": [
                "Spain",
                "Norway",
                "France",
                "Belgium",
                "EMBL",
                "Hungary",
                "Denmark"
            ],
            "elixirCommunity": [
                "3D-BioInfo"
            ],
            "link": [
                {
                    "url": "https://mmb.irbbarcelona.org/biobb/workflows#protein-conformational-ensembles-generation",
                    "type": [
                        "Other"
                    ],
                    "note": "Main web site (BioBB workflows)"
                },
                {
                    "url": "https://mmb.irbbarcelona.org/biobb/workflows/tutorials/flexdyn",
                    "type": [
                        "Other"
                    ],
                    "note": "Tutorial in HTML"
                },
                {
                    "url": "https://biobb-wf-flexdyn.readthedocs.io/en/latest/index.html",
                    "type": [
                        "Other"
                    ],
                    "note": "Tutorial in Read The Docs"
                },
                {
                    "url": "https://github.com/bioexcel/biobb_wf_flexdyn",
                    "type": [
                        "Repository"
                    ],
                    "note": "Source Code in GitHub"
                }
            ],
            "download": [
                {
                    "url": "https://github.com/bioexcel/biobb_wf_flexdyn",
                    "type": "Source code",
                    "note": null,
                    "version": "1.0"
                },
                {
                    "url": "https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_md_setup/master?filepath=biobb_wf_md_setup%2Fnotebooks%2Fbiobb_MDsetup_tutorial.ipynb",
                    "type": "VM image",
                    "note": "BioExcel Binder",
                    "version": "1.0"
                }
            ],
            "documentation": [
                {
                    "url": "https://biobb-wf-flexdyn.readthedocs.io/en/latest/?badge=latest",
                    "type": [
                        "Other"
                    ],
                    "note": "Read The Docs Workflow Documentation"
                }
            ],
            "publication": [
                {
                    "doi": "10.1038/s41597-019-0177-4",
                    "pmid": "31506435",
                    "pmcid": "PMC6736963",
                    "type": [
                        "Other"
                    ],
                    "version": null,
                    "note": "BioExcel Building Blocks (BioBB)",
                    "metadata": {
                        "title": "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows",
                        "abstract": "In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments.",
                        "date": "2019-12-01T00:00:00Z",
                        "citationCount": 28,
                        "authors": [
                            {
                                "name": "Andrio P."
                            },
                            {
                                "name": "Hospital A."
                            },
                            {
                                "name": "Conejero J."
                            },
                            {
                                "name": "Jorda L."
                            },
                            {
                                "name": "Del Pino M."
                            },
                            {
                                "name": "Codo L."
                            },
                            {
                                "name": "Soiland-Reyes S."
                            },
                            {
                                "name": "Goble C."
                            },
                            {
                                "name": "Lezzi D."
                            },
                            {
                                "name": "Badia R.M."
                            },
                            {
                                "name": "Orozco M."
                            },
                            {
                                "name": "Gelpi J.L."
                            }
                        ],
                        "journal": "Scientific Data"
                    }
                },
                {
                    "doi": "10.12688/f1000research.20559.1",
                    "pmid": "32566135",
                    "pmcid": "PMC7284151",
                    "type": [
                        "Other"
                    ],
                    "version": null,
                    "note": "3D-BioInfo, ELIXIR Structural Community",
                    "metadata": {
                        "title": "A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)",
                        "abstract": "Structural bioinformatics provides the scientific methods and tools to analyse, archive, validate, and present the biomolecular structure data generated by the structural biology community. It also provides an important link with the genomics community, as structural bioinformaticians also use the extensive sequence data to predict protein structures and their functional sites. A very broad and active community of structural bioinformaticians exists across Europe, and 3D-Bioinfo will establish formal platforms to address their needs and better integrate their activities and initiatives. Our mission will be to strengthen the ties with the structural biology research communities in Europe covering life sciences, as well as chemistry and physics and to bridge the gap between these researchers in order to fully realize the potential of structural bioinformatics. Our Community will also undertake dedicated educational, training and outreach efforts to facilitate this, bringing new insights and thus facilitating the development of much needed innovative applications e.g. for human health, drug and protein design. Our combined efforts will be of critical importance to keep the European research efforts competitive in this respect. Here we highlight the major European contributions to the field of structural bioinformatics, the most pressing challenges remaining and how Europe-wide interactions, enabled by ELIXIR and its platforms, will help in addressing these challenges and in coordinating structural bioinformatics resources across Europe. In particular, we present recent activities and future plans to consolidate an ELIXIR 3D-Bioinfo Community in structural bioinformatics and propose means to develop better links across the community. These include building new consortia, organising workshops to establish data standards and seeking community agreement on benchmark data sets and strategies. We also highlight existing and planned collaborations with other ELIXIR Communities and other European infrastructures, such as the structural biology community supported by Instruct-ERIC, with whom we have synergies and overlapping common interests.",
                        "date": "2020-01-01T00:00:00Z",
                        "citationCount": 8,
                        "authors": [
                            {
                                "name": "Orengo C."
                            },
                            {
                                "name": "Velankar S."
                            },
                            {
                                "name": "Wodak S."
                            },
                            {
                                "name": "Zoete V."
                            },
                            {
                                "name": "Bonvin A.M.J.J."
                            },
                            {
                                "name": "Elofsson A."
                            },
                            {
                                "name": "Feenstra K.A."
                            },
                            {
                                "name": "Gerloff D.L."
                            },
                            {
                                "name": "Hamelryck T."
                            },
                            {
                                "name": "Hancock J.M."
                            },
                            {
                                "name": "Helmer-Citterich M."
                            },
                            {
                                "name": "Hospital A."
                            },
                            {
                                "name": "Orozco M."
                            },
                            {
                                "name": "Perrakis A."
                            },
                            {
                                "name": "Rarey M."
                            },
                            {
                                "name": "Soares C."
                            },
                            {
                                "name": "Sussman J.L."
                            },
                            {
                                "name": "Thornton J.M."
                            },
                            {
                                "name": "Tuffery P."
                            },
                            {
                                "name": "Tusnady G."
                            },
                            {
                                "name": "Wierenga R."
                            },
                            {
                                "name": "Salminen T."
                            },
                            {
                                "name": "Schneider B."
                            }
                        ],
                        "journal": "F1000Research"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Adam Hospital",
                    "email": "adam.hospital@irbbarcelona.org",
                    "url": "https://www.irbbarcelona.org/en/research/adam-hospital",
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Primary contact",
                        "Developer",
                        "Documentor",
                        "Maintainer"
                    ],
                    "note": null
                },
                {
                    "name": "Genís Bayarri",
                    "email": "genis.bayarri@irbbarcelona.org",
                    "url": "https://www.irbbarcelona.org/en/research/genis-bayarri",
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Contributor",
                        "Maintainer"
                    ],
                    "note": null
                },
                {
                    "name": "3D-BioInfo",
                    "email": "katharina.heil@elixir-europe.org",
                    "url": "https://elixir-europe.org/communities/3d-bioinfo",
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Consortium",
                    "typeRole": [
                        "Provider"
                    ],
                    "note": null
                }
            ],
            "community": null,
            "owner": "adam.hospital@irbbarcelona.org",
            "additionDate": "2023-05-25T11:54:30.874289Z",
            "lastUpdate": "2023-05-25T11:54:30.877367Z",
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        },
        {
            "name": "LambdaPP",
            "description": "Fast and accessible protein-specific phenotype predictions.",
            "homepage": "http://embed.predictprotein.org",
            "biotoolsID": "lambdapp",
            "biotoolsCURIE": "biotools:lambdapp",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0267",
                            "term": "Protein secondary structure prediction"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0331",
                            "term": "Variant effect prediction"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3904",
                            "term": "Protein disorder prediction"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0474",
                            "term": "Protein structure prediction"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2044",
                                "term": "Sequence"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2291",
                                "term": "UniProt ID"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_3021",
                                "term": "UniProt accession"
                            },
                            "format": []
                        }
                    ],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Web application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_3474",
                    "term": "Machine learning"
                },
                {
                    "uri": "http://edamontology.org/topic_0625",
                    "term": "Genotype and phenotype"
                },
                {
                    "uri": "http://edamontology.org/topic_0082",
                    "term": "Structure prediction"
                },
                {
                    "uri": "http://edamontology.org/topic_3542",
                    "term": "Protein secondary structure"
                },
                {
                    "uri": "http://edamontology.org/topic_3510",
                    "term": "Protein sites, features and motifs"
                }
            ],
            "operatingSystem": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "language": [
                "Python"
            ],
            "license": "AFL-2.0",
            "collectionID": [],
            "maturity": null,
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://embed.predictprotein.org/#/Q9NZC2",
                    "type": [
                        "Other"
                    ],
                    "note": null
                }
            ],
            "download": [],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.1002/pro.4524",
                    "pmid": "36454227",
                    "pmcid": "PMC9793974",
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "LambdaPP: Fast and accessible protein-specific phenotype predictions",
                        "abstract": "The availability of accurate and fast artificial intelligence (AI) solutions predicting aspects of proteins are revolutionizing experimental and computational molecular biology. The webserver LambdaPP aspires to supersede PredictProtein, the first internet server making AI protein predictions available in 1992. Given a protein sequence as input, LambdaPP provides easily accessible visualizations of protein 3D structure, along with predictions at the protein level (GeneOntology, subcellular location), and the residue level (binding to metal ions, small molecules, and nucleotides; conservation; intrinsic disorder; secondary structure; alpha-helical and beta-barrel transmembrane segments; signal-peptides; variant effect) in seconds. The structure prediction provided by LambdaPP—leveraging ColabFold and computed in minutes—is based on MMseqs2 multiple sequence alignments. All other feature prediction methods are based on the pLM ProtT5. Queried by a protein sequence, LambdaPP computes protein and residue predictions almost instantly for various phenotypes, including 3D structure and aspects of protein function. LambdaPP is freely available for everyone to use under embed.predictprotein.org, the interactive results for the case study can be found under https://embed.predictprotein.org/o/Q9NZC2. The frontend of LambdaPP can be found on GitHub (github.com/sacdallago/embed.predictprotein.org), and can be freely used and distributed under the academic free use license (AFL-2). For high-throughput applications, all methods can be executed locally via the bio-embeddings (bioembeddings.com) python package, or docker image at ghcr.io/bioembeddings/bio_embeddings, which also includes the backend of LambdaPP.",
                        "date": "2023-01-01T00:00:00Z",
                        "citationCount": 0,
                        "authors": [
                            {
                                "name": "Olenyi T."
                            },
                            {
                                "name": "Marquet C."
                            },
                            {
                                "name": "Heinzinger M."
                            },
                            {
                                "name": "Kroger B."
                            },
                            {
                                "name": "Nikolova T."
                            },
                            {
                                "name": "Bernhofer M."
                            },
                            {
                                "name": "Sandig P."
                            },
                            {
                                "name": "Schutze K."
                            },
                            {
                                "name": "Littmann M."
                            },
                            {
                                "name": "Mirdita M."
                            },
                            {
                                "name": "Steinegger M."
                            },
                            {
                                "name": "Dallago C."
                            },
                            {
                                "name": "Rost B."
                            }
                        ],
                        "journal": "Protein Science"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Burkhard Rost",
                    "email": null,
                    "url": null,
                    "orcidid": "http://orcid.org/0000-0003-0179-8424",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": null,
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Christian Dallago",
                    "email": null,
                    "url": null,
                    "orcidid": "http://orcid.org/0000-0003-4650-6181",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": null,
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Tobias Olenyi",
                    "email": null,
                    "url": null,
                    "orcidid": "http://orcid.org/0000-0002-6315-0458",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": null,
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Céline Marquet",
                    "email": null,
                    "url": null,
                    "orcidid": "http://orcid.org/0000-0002-8691-5791",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": null,
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "Jennifer",
            "additionDate": "2023-03-24T00:03:01.606504Z",
            "lastUpdate": "2023-03-24T00:03:01.609353Z",
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        },
        {
            "name": "DeepTP",
            "description": "A Deep Learning Model for Thermophilic Protein Prediction.",
            "homepage": "http://www.YangLab-MI.org.cn/DeepTP",
            "biotoolsID": "deeptp",
            "biotoolsCURIE": "biotools:deeptp",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_3092",
                            "term": "Protein feature detection"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0477",
                            "term": "Protein modelling"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0253",
                            "term": "Sequence feature detection"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Script",
                "Web application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_3474",
                    "term": "Machine learning"
                },
                {
                    "uri": "http://edamontology.org/topic_0821",
                    "term": "Enzymes"
                },
                {
                    "uri": "http://edamontology.org/topic_3510",
                    "term": "Protein sites, features and motifs"
                },
                {
                    "uri": "http://edamontology.org/topic_0154",
                    "term": "Small molecules"
                },
                {
                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
                }
            ],
            "operatingSystem": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "language": [
                "Python"
            ],
            "license": "Not licensed",
            "collectionID": [],
            "maturity": null,
            "cost": null,
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://github.com/ZhaoDove/DeepTP_predictor",
                    "type": [
                        "Repository"
                    ],
                    "note": null
                }
            ],
            "download": [],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.3390/IJMS24032217",
                    "pmid": "36768540",
                    "pmcid": "PMC9917291",
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "DeepTP: A Deep Learning Model for Thermophilic Protein Prediction",
                        "abstract": "Thermophilic proteins have important value in the fields of biopharmaceuticals and enzyme engineering. Most existing thermophilic protein prediction models are based on traditional machine learning algorithms and do not fully utilize protein sequence information. To solve this problem, a deep learning model based on self-attention and multiple-channel feature fusion was proposed to predict thermophilic proteins, called DeepTP. First, a large new dataset consisting of 20,842 proteins was constructed. Second, a convolutional neural network and bidirectional long short-term memory network were used to extract the hidden features in protein sequences. Different weights were then assigned to features through self-attention, and finally, biological features were integrated to build a prediction model. In a performance comparison with existing methods, DeepTP had better performance and scalability in an independent balanced test set and validation set, with AUC values of 0.944 and 0.801, respectively. In the unbalanced test set, DeepTP had an average precision (AP) of 0.536. The tool is freely available.",
                        "date": "2023-02-01T00:00:00Z",
                        "citationCount": 0,
                        "authors": [
                            {
                                "name": "Zhao J."
                            },
                            {
                                "name": "Yan W."
                            },
                            {
                                "name": "Yang Y."
                            }
                        ],
                        "journal": "International Journal of Molecular Sciences"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Wenying Yan",
                    "email": "wyyan@suda.edu.cn",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0001-5016-575X",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Yang Yang",
                    "email": "yyang@suda.edu.cn",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-4397-8215",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "Chan019",
            "additionDate": "2023-03-18T08:32:48.899699Z",
            "lastUpdate": "2023-03-18T08:32:48.903981Z",
            "editPermission": {
                "type": "public",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        },
        {
            "name": "RCSB Protein Data Bank",
            "description": "Improved Annotation, Search, and Visualization of Membrane Protein Structures Archived in the PDB.",
            "homepage": "http://rcsb.org",
            "biotoolsID": "rcsb_pdb",
            "biotoolsCURIE": "biotools:rcsb_pdb",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0337",
                            "term": "Visualisation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3767",
                            "term": "Protein identification"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3431",
                            "term": "Deposition"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0310",
                            "term": "Sequence assembly"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Database portal"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0820",
                    "term": "Membrane and lipoproteins"
                },
                {
                    "uri": "http://edamontology.org/topic_0154",
                    "term": "Small molecules"
                },
                {
                    "uri": "http://edamontology.org/topic_2814",
                    "term": "Protein structure analysis"
                },
                {
                    "uri": "http://edamontology.org/topic_0821",
                    "term": "Enzymes"
                },
                {
                    "uri": "http://edamontology.org/topic_3510",
                    "term": "Protein sites, features and motifs"
                }
            ],
            "operatingSystem": [
                "Mac",
                "Linux",
                "Windows"
            ],
            "language": [],
            "license": null,
            "collectionID": [],
            "maturity": null,
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [],
            "download": [],
            "documentation": [
                {
                    "url": "http://data.rcsb.org",
                    "type": [
                        "API documentation"
                    ],
                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1093/BIOINFORMATICS/BTAB813",
                    "pmid": "34864908",
                    "pmcid": "PMC8826025",
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "RCSB Protein Data Bank: Improved annotation, search and visualization of membrane protein structures archived in the PDB",
                        "abstract": "© 2021 The Author(s) 2021. Published by Oxford University Press.Motivation: Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task. Results: We present recent improvements to the RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide a wealth of new membrane protein annotations integrated from four external resources: OPM, PDBTM, MemProtMD and mpstruc. We have substantially enhanced the presentation of data on membrane proteins. The number of membrane proteins with annotations available on rcsb.org was increased by ∼80%. Users can search for these annotations, explore corresponding tree hierarchies, display membrane segments at the 1D amino acid sequence level, and visualize the predicted location of the membrane layer in 3D.",
                        "date": "2022-03-01T00:00:00Z",
                        "citationCount": 10,
                        "authors": [
                            {
                                "name": "Bittrich S."
                            },
                            {
                                "name": "Rose Y."
                            },
                            {
                                "name": "Segura J."
                            },
                            {
                                "name": "Lowe R."
                            },
                            {
                                "name": "Westbrook J.D."
                            },
                            {
                                "name": "Duarte J.M."
                            },
                            {
                                "name": "Burley S.K."
                            }
                        ],
                        "journal": "Bioinformatics"
                    }
                },
                {
                    "doi": "10.1093/NAR/GKAC1077",
                    "pmid": "36420884",
                    "pmcid": "PMC9825554",
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning",
                        "abstract": "© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a 'living data resource.' Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.",
                        "date": "2023-01-06T00:00:00Z",
                        "citationCount": 0,
                        "authors": [
                            {
                                "name": "Burley S.K."
                            },
                            {
                                "name": "Bhikadiya C."
                            },
                            {
                                "name": "Bi C."
                            },
                            {
                                "name": "Bittrich S."
                            },
                            {
                                "name": "Chao H."
                            },
                            {
                                "name": "Chen L."
                            },
                            {
                                "name": "Craig P.A."
                            },
                            {
                                "name": "Crichlow G.V."
                            },
                            {
                                "name": "Dalenberg K."
                            },
                            {
                                "name": "Duarte J.M."
                            },
                            {
                                "name": "Dutta S."
                            },
                            {
                                "name": "Fayazi M."
                            },
                            {
                                "name": "Feng Z."
                            },
                            {
                                "name": "Flatt J.W."
                            },
                            {
                                "name": "Ganesan S."
                            },
                            {
                                "name": "Ghosh S."
                            },
                            {
                                "name": "Goodsell D.S."
                            },
                            {
                                "name": "Green R.K."
                            },
                            {
                                "name": "Guranovic V."
                            },
                            {
                                "name": "Henry J."
                            },
                            {
                                "name": "Hudson B.P."
                            },
                            {
                                "name": "Khokhriakov I."
                            },
                            {
                                "name": "Lawson C.L."
                            },
                            {
                                "name": "Liang Y."
                            },
                            {
                                "name": "Lowe R."
                            },
                            {
                                "name": "Peisach E."
                            },
                            {
                                "name": "Persikova I."
                            },
                            {
                                "name": "Piehl D.W."
                            },
                            {
                                "name": "Rose Y."
                            },
                            {
                                "name": "Sali A."
                            },
                            {
                                "name": "Segura J."
                            },
                            {
                                "name": "Sekharan M."
                            },
                            {
                                "name": "Shao C."
                            },
                            {
                                "name": "Vallat B."
                            },
                            {
                                "name": "Voigt M."
                            },
                            {
                                "name": "Webb B."
                            },
                            {
                                "name": "Westbrook J.D."
                            },
                            {
                                "name": "Whetstone S."
                            },
                            {
                                "name": "Young J.Y."
                            },
                            {
                                "name": "Zalevsky A."
                            },
                            {
                                "name": "Zardecki C."
                            }
                        ],
                        "journal": "Nucleic acids research"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Sebastian Bittrich",
                    "email": "sebastian.bittrich@rcsb.org",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-3576-0387",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "John D Westbrook",
                    "email": null,
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-6686-5475",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": null,
                    "typeRole": [],
                    "note": null
                },
                {
                    "name": "Jose M Duarte",
                    "email": null,
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-9544-5621",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": null,
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "Jennifer",
            "additionDate": "2022-05-17T17:56:11.990250Z",
            "lastUpdate": "2023-01-30T22:53:45.393584Z",
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "validated": 1,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": "tool"
        },
        {
            "name": "GPCRDB",
            "description": "GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs). GPCRdb curates sequence alignments, structures and receptor mutations from literature. Interactive diagrams visualise receptor residues (e.g. snakeplot and helix box plot) and relationships (e.g phylogenetic trees).",
            "homepage": "https://gpcrdb.org",
            "biotoolsID": "gpcrdb",
            "biotoolsCURIE": "biotools:gpcrdb",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0346",
                            "term": "Sequence similarity search"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0477",
                            "term": "Protein modelling"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2928",
                            "term": "Alignment"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0337",
                            "term": "Visualisation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2451",
                            "term": "Sequence comparison"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0240",
                            "term": "Sequence motif comparison"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0291",
                            "term": "Sequence clustering"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2990",
                            "term": "Classification"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2974",
                                "term": "Protein sequence (raw)"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1381",
                                "term": "Sequence alignment (pair)"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0857",
                                "term": "Sequence search results"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1707",
                                "term": "Phylogenetic tree image"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0872",
                                "term": "Phylogenetic tree"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2884",
                                "term": "Plot"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2886",
                                "term": "Protein sequence record"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1277",
                                "term": "Protein features"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
                            },
                            "format": []
                        }
                    ],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Web application",
                "Database portal",
                "Web service"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_1317",
                    "term": "Structural biology"
                },
                {
                    "uri": "http://edamontology.org/topic_3293",
                    "term": "Phylogenetics"
                },
                {
                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
                },
                {
                    "uri": "http://edamontology.org/topic_3542",
                    "term": "Protein secondary structure"
                },
                {
                    "uri": "http://edamontology.org/topic_3510",
                    "term": "Protein sites, features and motifs"
                },
                {
                    "uri": "http://edamontology.org/topic_3534",
                    "term": "Protein binding sites"
                },
                {
                    "uri": "http://edamontology.org/topic_2275",
                    "term": "Molecular modelling"
                },
                {
                    "uri": "http://edamontology.org/topic_0082",
                    "term": "Structure prediction"
                }
            ],
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "language": [
                "Python",
                "SQL"
            ],
            "license": null,
            "collectionID": [],
            "maturity": "Mature",
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://github.com/protwis/protwis",
                    "type": [
                        "Repository"
                    ],
                    "note": "Source of the framework that runs GPCRdb"
                },
                {
                    "url": "https://github.com/protwis/gpcrdb_data",
                    "type": [
                        "Repository"
                    ],
                    "note": "Data repository for the GPCRdb"
                },
                {
                    "url": "https://github.com/protwis/protwis/issues",
                    "type": [
                        "Issue tracker"
                    ],
                    "note": "Issue tracker for the GPCRdb"
                }
            ],
            "download": [],
            "documentation": [
                {
                    "url": "https://docs.gpcrdb.org",
                    "type": [
                        "General"
                    ],
                    "note": "Documentation of the GPCRdb ranging from a general introduction to tool descriptions and development instructions."
                },
                {
                    "url": "https://gpcrdb.org/services/reference/",
                    "type": [
                        "API documentation"
                    ],
                    "note": "Documentation for the REST web services"
                }
            ],
            "publication": [
                {
                    "doi": "10.1093/nar/gkv1178",
                    "pmid": null,
                    "pmcid": null,
                    "type": [],
                    "version": null,
                    "note": "2016 GPCRdb publication",
                    "metadata": {
                        "title": "GPCRdb: An information system for G protein-coupled receptors",
                        "abstract": "© The Author(s) 2015.Recent developments in G protein-coupled receptor (GPCR) structural biology and pharmacology have greatly enhanced our knowledge of receptor structure-function relations, and have helped improve the scientific foundation for drug design studies. The GPCR database, GPCRdb, serves a dual role in disseminating and enabling new scientific developments by providing reference data, analysis tools and interactive diagrams. This paper highlights new features in the fifth major GPCRdb release: (i) GPCR crystal structure browsing, superposition and display of ligand interactions; (ii) direct deposition by users of point mutations and their effects on ligand binding; (iii) refined snake and helix box residue diagram looks; and (iii) phylogenetic trees with receptor classification colour schemes. Under the hood, the entire GPCRdb front- and back-ends have been recoded within one infrastructure, ensuring a smooth browsing experience and development. GPCRdb is available at http://www.gpcrdb.org/ and it's open source code at https://bitbucket.org/gpcr/protwis.",
                        "date": "2016-01-01T00:00:00Z",
                        "citationCount": 196,
                        "authors": [
                            {
                                "name": "Isberg V."
                            },
                            {
                                "name": "Mordalski S."
                            },
                            {
                                "name": "Munk C."
                            },
                            {
                                "name": "Rataj K."
                            },
                            {
                                "name": "Harpsoe K."
                            },
                            {
                                "name": "Hauser A.S."
                            },
                            {
                                "name": "Vroling B."
                            },
                            {
                                "name": "Bojarski A.J."
                            },
                            {
                                "name": "Vriend G."
                            },
                            {
                                "name": "Gloriam D.E."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                },
                {
                    "doi": "10.1093/nar/gkaa1080",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Other"
                    ],
                    "version": null,
                    "note": "2021 GPCRdb publication",
                    "metadata": {
                        "title": "GPCRdb in 2021: Integrating GPCR sequence, structure and function",
                        "abstract": "© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.G protein-coupled receptors (GPCRs) form both the largest family of membrane proteins and drug targets, mediating the action of one-third of medicines. The GPCR database, GPCRdb serves >4 000 researchers every month and offers reference data, analysis of own or literature data, experiment design and dissemination of published datasets. Here, we describe new and updated GPCRdb resources with a particular focus on integration of sequence, structure and function. GPCRdb contains all human non-olfactory GPCRs (and >27 000 orthologs), G-proteins and arrestins. It includes over 2 000 drug and in-trial agents and nearly 200 000 ligands with activity and availability data. GPCRdb annotates all published GPCR structures (updated monthly), which are also offered in a refined version (with re-modeled missing/distorted regions and reverted mutations) and provides structure models of all human non-olfactory receptors in inactive, intermediate and active states. Mutagenesis data in the GPCRdb spans natural genetic variants, GPCR-G protein interfaces, ligand sites and thermostabilising mutations. A new sequence signature tool for identification of functional residue determinants has been added and two data driven tools to design ligand site mutations and constructs for structure determination have been updated extending their coverage of receptors and modifications. The GPCRdb is available at https://gpcrdb.org.",
                        "date": "2021-01-08T00:00:00Z",
                        "citationCount": 129,
                        "authors": [
                            {
                                "name": "Kooistra A.J."
                            },
                            {
                                "name": "Mordalski S."
                            },
                            {
                                "name": "Pandy-Szekeres G."
                            },
                            {
                                "name": "Esguerra M."
                            },
                            {
                                "name": "Mamyrbekov A."
                            },
                            {
                                "name": "Munk C."
                            },
                            {
                                "name": "Keseru G.M."
                            },
                            {
                                "name": "Gloriam D.E."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                },
                {
                    "doi": "10.1093/nar/gkx1109",
                    "pmid": null,
                    "pmcid": null,
                    "type": [],
                    "version": null,
                    "note": "2018 GPCRdb publication",
                    "metadata": {
                        "title": "GPCRdb in 2018: Adding GPCR structure models and ligands",
                        "abstract": "© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.G protein-coupled receptors are the most abundant mediators of both human signalling processes and therapeutic effects. Herein, we report GPCRome-wide homology models of unprecedented quality, and roughly 150 000 GPCR ligands with data on biological activities and commercial availability. Based on the strategy of 'Less model - more Xtal', each model exploits both a main template and alternative local templates. This achieved higher similarity to new structures than any of the existing resources, and refined crystal structures with missing or distorted regions. Models are provided for inactive, intermediate and active states - except for classes C and F that so far only have inactive templates. The ligand database has separate browsers for: (i) target selection by receptor, family or class, (ii) ligand filtering based on cross-experiment activities (min, max and mean) or chemical properties, (iii) ligand source data and (iv) commercial availability. SMILES structures and activity spreadsheets can be downloaded for further processing. Furthermore, three recent landmark publications on GPCR drugs, G protein selectivity and genetic variants have been accompanied with resources that now let readers view and analyse the findings themselves in GPCRdb. Altogether, this update will enable scientific investigation for the wider GPCR community. GPCRdb is available at http://www.gpcrdb.org.",
                        "date": "2018-01-01T00:00:00Z",
                        "citationCount": 299,
                        "authors": [
                            {
                                "name": "Pandy-Szekeres G."
                            },
                            {
                                "name": "Munk C."
                            },
                            {
                                "name": "Tsonkov T.M."
                            },
                            {
                                "name": "Mordalski S."
                            },
                            {
                                "name": "Harpsoe K."
                            },
                            {
                                "name": "Hauser A.S."
                            },
                            {
                                "name": "Bojarski A.J."
                            },
                            {
                                "name": "Gloriam D.E."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                },
                {
                    "doi": "10.1038/s41586-020-2888-2",
                    "pmid": null,
                    "pmcid": null,
                    "type": [],
                    "version": null,
                    "note": "GPCR isoform resource as available in the GPCRdb",
                    "metadata": {
                        "title": "Combinatorial expression of GPCR isoforms affects signalling and drug responses",
                        "abstract": "© 2020, The Author(s), under exclusive licence to Springer Nature Limited.G-protein-coupled receptors (GPCRs) are membrane proteins that modulate physiology across human tissues in response to extracellular signals. GPCR-mediated signalling can differ because of changes in the sequence1,2 or expression3 of the receptors, leading to signalling bias when comparing diverse physiological systems4. An underexplored source of such bias is the generation of functionally diverse GPCR isoforms with different patterns of expression across different tissues. Here we integrate data from human tissue-level transcriptomes, GPCR sequences and structures, proteomics, single-cell transcriptomics, population-wide genetic association studies and pharmacological experiments. We show how a single GPCR gene can diversify into several isoforms with distinct signalling properties, and how unique isoform combinations expressed in different tissues can generate distinct signalling states. Depending on their structural changes and expression patterns, some of the detected isoforms may influence cellular responses to drugs and represent new targets for developing drugs with improved tissue selectivity. Our findings highlight the need to move from a canonical to a context-specific view of GPCR signalling that considers how combinatorial expression of isoforms in a particular cell type, tissue or organism collectively influences receptor signalling and drug responses.",
                        "date": "2020-11-26T00:00:00Z",
                        "citationCount": 39,
                        "authors": [
                            {
                                "name": "Marti-Solano M."
                            },
                            {
                                "name": "Crilly S.E."
                            },
                            {
                                "name": "Malinverni D."
                            },
                            {
                                "name": "Munk C."
                            },
                            {
                                "name": "Harris M."
                            },
                            {
                                "name": "Pearce A."
                            },
                            {
                                "name": "Quon T."
                            },
                            {
                                "name": "Mackenzie A.E."
                            },
                            {
                                "name": "Wang X."
                            },
                            {
                                "name": "Peng J."
                            },
                            {
                                "name": "Tobin A.B."
                            },
                            {
                                "name": "Ladds G."
                            },
                            {
                                "name": "Milligan G."
                            },
                            {
                                "name": "Gloriam D.E."
                            },
                            {
                                "name": "Puthenveedu M.A."
                            },
                            {
                                "name": "Babu M.M."
                            }
                        ],
                        "journal": "Nature"
                    }
                },
                {
                    "doi": "10.1038/s41592-018-0302-x",
                    "pmid": null,
                    "pmcid": null,
                    "type": [],
                    "version": null,
                    "note": "GPCR construct design tool as available in the GPCRdb",
                    "metadata": {
                        "title": "An online resource for GPCR structure determination and analysis",
                        "abstract": "© 2019, Springer Nature America, Inc.G-protein-coupled receptors (GPCRs) transduce physiological and sensory stimuli into appropriate cellular responses and mediate the actions of one-third of drugs. GPCR structural studies have revealed the general bases of receptor activation, signaling, drug action and allosteric modulation, but so far cover only 13% of nonolfactory receptors. We broadly surveyed the receptor modifications/engineering and methods used to produce all available GPCR crystal and cryo-electron microscopy (cryo-EM) structures, and present an interactive resource integrated in GPCRdb (http://www.gpcrdb.org) to assist users in designing constructs and browsing appropriate experimental conditions for structure studies.",
                        "date": "2019-02-01T00:00:00Z",
                        "citationCount": 85,
                        "authors": [
                            {
                                "name": "Munk C."
                            },
                            {
                                "name": "Mutt E."
                            },
                            {
                                "name": "Isberg V."
                            },
                            {
                                "name": "Nikolajsen L.F."
                            },
                            {
                                "name": "Bibbe J.M."
                            },
                            {
                                "name": "Flock T."
                            },
                            {
                                "name": "Hanson M.A."
                            },
                            {
                                "name": "Stevens R.C."
                            },
                            {
                                "name": "Deupi X."
                            },
                            {
                                "name": "Gloriam D.E."
                            }
                        ],
                        "journal": "Nature Methods"
                    }
                },
                {
                    "doi": "10.1093/nar/gkac1013",
                    "pmid": "36395823",
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": "2023 GPCRdb publication",
                    "metadata": null
                },
                {
                    "doi": "10.1038/s41594-021-00675-6",
                    "pmid": "34759374",
                    "pmcid": null,
                    "type": [],
                    "version": null,
                    "note": "An online GPCR structure analysis platform",
                    "metadata": {
                        "title": "An online GPCR structure analysis platform",
                        "abstract": "© 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.We present an online, interactive platform for comparative analysis of all available G-protein coupled receptor (GPCR) structures while correlating to functional data. The comprehensive platform encompasses structure similarity, secondary structure, protein backbone packing and movement, residue–residue contact networks, amino acid properties and prospective design of experimental mutagenesis studies. This lets any researcher tap the potential of sophisticated structural analyses enabling a plethora of basic and applied receptor research studies.",
                        "date": "2021-11-01T00:00:00Z",
                        "citationCount": 3,
                        "authors": [
                            {
                                "name": "Kooistra A.J."
                            },
                            {
                                "name": "Munk C."
                            },
                            {
                                "name": "Hauser A.S."
                            },
                            {
                                "name": "Gloriam D.E."
                            }
                        ],
                        "journal": "Nature Structural and Molecular Biology"
                    }
                }
            ],
            "credit": [
                {
                    "name": "GPCRDB",
                    "email": "info@gpcr.org",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Project",
                    "typeRole": [
                        "Provider"
                    ],
                    "note": "Contact for general and support questions regarding the GPCRdb"
                },
                {
                    "name": "David Gloriam",
                    "email": null,
                    "url": "https://drug.ku.dk/staff/?pure=en/persons/352279",
                    "orcidid": "https://orcid.org/0000-0002-4299-7561",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Primary contact"
                    ],
                    "note": "Head of the GPCRdb"
                }
            ],
            "community": null,
            "owner": "GPCRDB",
            "additionDate": "2015-02-04T09:25:19Z",
            "lastUpdate": "2022-12-22T08:35:09.692744Z",
            "editPermission": {
                "type": "group",
                "authors": [
                    "AJK_dev"
                ]
            },
            "validated": 1,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": null
        },
        {
            "name": "Phobius (EBI)",
            "description": "Predict transmembrane topology and signal peptides from the amino acid sequence of a protein.",
            "homepage": "http://www.ebi.ac.uk/Tools/pfa/phobius/",
            "biotoolsID": "phobius",
            "biotoolsCURIE": "biotools:phobius",
            "version": [
                "1"
            ],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0418",
                            "term": "Protein signal peptide detection"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0269",
                            "term": "Transmembrane protein prediction"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1277",
                                "term": "Protein features"
                            },
                            "format": []
                        }
                    ],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Web application",
                "Web service"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0160",
                    "term": "Sequence sites, features and motifs"
                },
                {
                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
                },
                {
                    "uri": "http://edamontology.org/topic_0820",
                    "term": "Membrane and lipoproteins"
                },
                {
                    "uri": "http://edamontology.org/topic_0736",
                    "term": "Protein folds and structural domains"
                },
                {
                    "uri": "http://edamontology.org/topic_3510",
                    "term": "Protein sites, features and motifs"
                }
            ],
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "language": [],
            "license": null,
            "collectionID": [
                "EBI Tools",
                "Job Dispatcher Tools"
            ],
            "maturity": null,
            "cost": null,
            "accessibility": null,
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "http://www.ebi.ac.uk/support/",
                    "type": [
                        "Helpdesk"
                    ],
                    "note": null
                }
            ],
            "download": [
                {
                    "url": "https://phobius.sbc.su.se/",
                    "type": "Downloads page",
                    "note": null,
                    "version": null
                }
            ],
            "documentation": [
                {
                    "url": "http://www.ebi.ac.uk/about/terms-of-use",
                    "type": [
                        "Terms of use"
                    ],
                    "note": null
                },
                {
                    "url": "http://www.ebi.ac.uk/Tools/pfa/phobius/",
                    "type": [
                        "General"
                    ],
                    "note": null
                },
                {
                    "url": "https://phobius.sbc.su.se/",
                    "type": [
                        "General"
                    ],
                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1016/j.jmb.2004.03.016",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "A combined transmembrane topology and signal peptide prediction method",
                        "abstract": "An inherent problem in transmembrane protein topology prediction and signal peptide prediction is the high similarity between the hydrophobic regions of a transmembrane helix and that of a signal peptide, leading to cross-reaction between the two types of predictions. To improve predictions further, it is therefore important to make a predictor that aims to discriminate between the two classes. In addition, topology information can be gained when successfully predicting a signal peptide leading a transmembrane protein since it dictates that the N terminus of the mature protein must be on the non-cytoplasmic side of the membrane. Here, we present Phobius, a combined transmembrane protein topology and signal peptide predictor. The predictor is based on a hidden Markov model (HMM) that models the different sequence regions of a signal peptide and the different regions of a transmembrane protein in a series of interconnected states. Training was done on a newly assembled and curated dataset. Compared to TMHMM and SignalP, errors coming from cross-prediction between transmembrane segments and signal peptides were reduced substantially by Phobius. False classifications of signal peptides were reduced from 26.1% to 3.9% and false classifications of transmembrane helices were reduced from 19.0% to 7.7%. Phobius was applied to the proteomes of Homo sapiens and Escherichia coli. Here we also noted a drastic reduction of false classifications compared to TMHMM/SignalP, suggesting that Phobius is well suited for whole-genome annotation of signal peptides and transmembrane regions. The method is available at http://phobius.cgb.ki.se/ as well as at http://phobius.binf.ku.dk/ © 2004 Elsevier Ltd. All rights reserved.",
                        "date": "2004-05-14T00:00:00Z",
                        "citationCount": 1614,
                        "authors": [
                            {
                                "name": "Kall L."
                            },
                            {
                                "name": "Krogh A."
                            },
                            {
                                "name": "Sonnhammer E.L.L."
                            }
                        ],
                        "journal": "Journal of Molecular Biology"
                    }
                },
                {
                    "doi": "10.1093/nar/gkac240",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Other"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "Search and sequence analysis tools services from EMBL-EBI in 2022",
                        "abstract": "© 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.",
                        "date": "2022-07-05T00:00:00Z",
                        "citationCount": 64,
                        "authors": [
                            {
                                "name": "Madeira F."
                            },
                            {
                                "name": "Pearce M."
                            },
                            {
                                "name": "Tivey A.R.N."
                            },
                            {
                                "name": "Basutkar P."
                            },
                            {
                                "name": "Lee J."
                            },
                            {
                                "name": "Edbali O."
                            },
                            {
                                "name": "Madhusoodanan N."
                            },
                            {
                                "name": "Kolesnikov A."
                            },
                            {
                                "name": "Lopez R."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Erik Sonnhammer",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Developer"
                    ],
                    "note": null
                },
                {
                    "name": "Stockholm Bioinformatics Center",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Institute",
                    "typeRole": [
                        "Provider"
                    ],
                    "note": null
                },
                {
                    "name": "EMBL-EBI",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Institute",
                    "typeRole": [
                        "Provider"
                    ],
                    "note": null
                },
                {
                    "name": "Job Dispatcher",
                    "email": null,
                    "url": "https://www.ebi.ac.uk/Tools/jdispatcher",
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Project",
                    "typeRole": [
                        "Primary contact"
                    ],
                    "note": null
                }
            ],
            "community": null,
            "owner": "biomadeira",
            "additionDate": "2015-01-29T15:48:07Z",
            "lastUpdate": "2022-11-02T15:50:21.116676Z",
            "editPermission": {
                "type": "group",
                "authors": [
                    "nandana",
                    "biomadeira"
                ]
            },
            "validated": 1,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": null
        }
    ]
}