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            "name": "VarGenius",
            "description": "VarGenius is a platform for analysis of variants from DNA sequencing data. Currently it can be used for WES and Panels. Starting from fastq files it can execute the GATK Best Practices pipeline doing both single calling and joint calling. Then it executes Annovar for variant annotation and generates a readable output in tabular and XLS format. All the data extracted from the samples (variants, genotypes, etc..) are uploaded into a Postgres database which can be used for further downstream analyses.",
            "homepage": "https://github.com/frankMusacchia/VarGenius",
            "biotoolsID": "VarGenius",
            "biotoolsCURIE": "biotools:VarGenius",
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                "1.0"
            ],
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                {
                    "biotoolsID": "vargenius-hzd",
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                }
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            "function": [],
            "toolType": [
                "Command-line tool"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_2533",
                    "term": "DNA mutation"
                }
            ],
            "operatingSystem": [
                "Linux"
            ],
            "language": [
                "R",
                "Perl"
            ],
            "license": null,
            "collectionID": [],
            "maturity": "Mature",
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [
                "Tools"
            ],
            "elixirNode": [
                "Italy"
            ],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://groups.google.com/forum/#!forum/VarGenius",
                    "type": [
                        "Helpdesk"
                    ],
                    "note": null
                }
            ],
            "download": [
                {
                    "url": "https://github.com/frankMusacchia/VarGenius",
                    "type": "Source code",
                    "note": null,
                    "version": "1.0"
                }
            ],
            "documentation": [
                {
                    "url": "https://github.com/frankMusacchia/VarGenius/tree/master/GUIDE",
                    "type": [
                        "Installation instructions"
                    ],
                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1186/s12859-018-2532-4",
                    "pmid": "30541431",
                    "pmcid": "PMC6291943",
                    "type": [
                        "Primary",
                        "Benchmarking study"
                    ],
                    "version": "1.0",
                    "note": null,
                    "metadata": {
                        "title": "VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data through a PostgreSQL database",
                        "abstract": "© 2018 The Author(s).Background: Targeted resequencing has become the most used and cost-effective approach for identifying causative mutations of Mendelian diseases both for diagnostics and research purposes. Due to very rapid technological progress, NGS laboratories are expanding their capabilities to address the increasing number of analyses. Several open source tools are available to build a generic variant calling pipeline, but a tool able to simultaneously execute multiple analyses, organize, and categorize the samples is still missing. Results: Here we describe VarGenius, a Linux based command line software able to execute customizable pipelines for the analysis of multiple targeted resequencing data using parallel computing. VarGenius provides a database to store the output of the analysis (calling quality statistics, variant annotations, internal allelic variant frequencies) and sample information (personal data, genotypes, phenotypes). VarGenius can also perform the \"joint analysis\" of hundreds of samples with a single command, drastically reducing the time for the configuration and execution of the analysis. VarGenius executes the standard pipeline of the Genome Analysis Tool-Kit (GATK) best practices (GBP) for germinal variant calling, annotates the variants using Annovar, and generates a user-friendly output displaying the results through a web page. VarGenius has been tested on a parallel computing cluster with 52 machines with 120GB of RAM each. Under this configuration, a 50 M whole exome sequencing (WES) analysis for a family was executed in about 7h (trio or quartet); a joint analysis of 30 WES in about 24 h and the parallel analysis of 34 single samples from a 1 M panel in about 2 h. Conclusions: We developed VarGenius, a \"master\" tool that faces the increasing demand of heterogeneous NGS analyses and allows maximum flexibility for downstream analyses. It paves the way to a different kind of analysis, centered on cohorts rather than on singleton. Patient and variant information are stored into the database and any output file can be accessed programmatically. VarGenius can be used for routine analyses by biomedical researchers with basic Linux skills providing additional flexibility for computational biologists to develop their own algorithms for the comparison and analysis of data. The software is freely available at: https://github.com/frankMusacchia/VarGenius",
                        "date": "2018-12-12T00:00:00Z",
                        "citationCount": 8,
                        "authors": [
                            {
                                "name": "Musacchia F."
                            },
                            {
                                "name": "Ciolfi A."
                            },
                            {
                                "name": "Mutarelli M."
                            },
                            {
                                "name": "Bruselles A."
                            },
                            {
                                "name": "Castello R."
                            },
                            {
                                "name": "Pinelli M."
                            },
                            {
                                "name": "Basu S."
                            },
                            {
                                "name": "Banfi S."
                            },
                            {
                                "name": "Casari G."
                            },
                            {
                                "name": "Tartaglia M."
                            },
                            {
                                "name": "Nigro V."
                            },
                            {
                                "name": "Torella A."
                            },
                            {
                                "name": "Esposito G."
                            },
                            {
                                "name": "Cappuccio G."
                            },
                            {
                                "name": "Mancano G."
                            },
                            {
                                "name": "Maitz S."
                            },
                            {
                                "name": "Brunetti-Pierri N."
                            },
                            {
                                "name": "Parenti G."
                            },
                            {
                                "name": "Selicorni A."
                            }
                        ],
                        "journal": "BMC Bioinformatics"
                    }
                }
            ],
            "credit": [
                {
                    "name": "ELIXIR-ITA-TELETHON",
                    "email": "f.musacchia@tigem.it",
                    "url": null,
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                    ],
                    "note": null
                }
            ],
            "community": null,
            "owner": "FrankMusacchia",
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        },
        {
            "name": "mirKit",
            "description": "miRkit is an open source framework written in R, that allows for the comprehensive analysis of RT-PCR data, from the processing of raw data to a functional analysis of the produced results. The main goal of the tool is to provide an assessment of the samples’ quality, perform data normalization by endogenous and exogenous miRNAs, and facilitate differential and functional enrichment analysis. The tool offers fast execution times with low memory usage, can perform the full analysis from the raw RT-PCR data to functional analysis of targeted genes, and is specifically designed to support the popular miScript miRNA PCR Array (Qiagen) technology.",
            "homepage": "https://github.com/BiodataAnalysisGroup/miRkit",
            "biotoolsID": "mirkit",
            "biotoolsCURIE": "biotools:mirkit",
            "version": [
                "1.0"
            ],
            "otherID": [],
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            "operatingSystem": [],
            "language": [],
            "license": "MIT",
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            "maturity": "Mature",
            "cost": "Free of charge",
            "accessibility": "Open access",
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            "elixirNode": [],
            "elixirCommunity": [],
            "link": [],
            "download": [
                {
                    "url": "https://github.com/BiodataAnalysisGroup/miRkit",
                    "type": "Source code",
                    "note": null,
                    "version": "1.0"
                }
            ],
            "documentation": [
                {
                    "url": "https://github.com/BiodataAnalysisGroup/miRkit/blob/main/README.md",
                    "type": [
                        "Quick start guide"
                    ],
                    "note": null
                }
            ],
            "publication": [],
            "credit": [
                {
                    "name": "Fotis Psomopoulos",
                    "email": "fpsom@certh.gr",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-0222-4273",
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            "owner": "fpsom",
            "additionDate": "2021-09-20T06:49:28.552326Z",
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        },
        {
            "name": "VIQoR",
            "description": "VIQoR, is a user-friendly web service for Visually supervised protein Inference and protein Quantification implemented in R. The Shiny web interface integrates the post-identification processes involved in protein inference and relative protein abundance summarization, along with smart and novel interactive visualization modules to support the common researchers with a straight-forward tool for protein quantification, data browsing and data inspection.",
            "homepage": "http://computproteomics.bmb.sdu.dk:8192/app_direct/VIQoR/",
            "biotoolsID": "viqor",
            "biotoolsCURIE": "biotools:viqor",
            "version": [
                "1.0"
            ],
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                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_1812",
                            "term": "Parsing"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3695",
                            "term": "Filtering"
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                        {
                            "uri": "http://edamontology.org/operation_3435",
                            "term": "Standardisation and normalisation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2429",
                            "term": "Mapping"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3767",
                            "term": "Protein identification"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3925",
                            "term": "Network visualisation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3630",
                            "term": "Protein quantification"
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                        {
                            "uri": "http://edamontology.org/operation_3463",
                            "term": "Expression correlation analysis"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0571",
                            "term": "Expression data visualisation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0531",
                            "term": "Heat map generation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2938",
                            "term": "Dendrogram visualisation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3184",
                            "term": "Sequence assembly visualisation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2536",
                                "term": "Mass spectrometry data"
                            },
                            "format": [
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                                    "uri": "http://edamontology.org/format_3752",
                                    "term": "CSV"
                                },
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                                    "uri": "http://edamontology.org/format_2330",
                                    "term": "Textual format"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1233",
                                "term": "Sequence set (protein)"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
                                },
                                {
                                    "uri": "http://edamontology.org/format_2330",
                                    "term": "Textual format"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2536",
                                "term": "Mass spectrometry data"
                            },
                            "format": [
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                                    "uri": "http://edamontology.org/format_3752",
                                    "term": "CSV"
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                            ]
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                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2603",
                                "term": "Expression data"
                            },
                            "format": [
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                                    "term": "CSV"
                                }
                            ]
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                                "uri": "http://edamontology.org/data_2884",
                                "term": "Plot"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3508",
                                    "term": "PDF"
                                },
                                {
                                    "uri": "http://edamontology.org/format_2331",
                                    "term": "HTML"
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                            ]
                        }
                    ],
                    "note": null,
                    "cmd": null
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            ],
            "toolType": [
                "Web service",
                "Script"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
                },
                {
                    "uri": "http://edamontology.org/topic_3520",
                    "term": "Proteomics experiment"
                },
                {
                    "uri": "http://edamontology.org/topic_0092",
                    "term": "Data visualisation"
                },
                {
                    "uri": "http://edamontology.org/topic_0108",
                    "term": "Protein expression"
                },
                {
                    "uri": "http://edamontology.org/topic_0601",
                    "term": "Protein modifications"
                }
            ],
            "operatingSystem": [
                "Windows",
                "Linux",
                "Mac"
            ],
            "language": [
                "R",
                "JavaScript"
            ],
            "license": "Apache-2.0",
            "collectionID": [
                "Proteomics"
            ],
            "maturity": "Mature",
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [
                "Denmark"
            ],
            "elixirCommunity": [
                "Proteomics"
            ],
            "link": [
                {
                    "url": "https://bitbucket.org/vtsiamis/viqor/",
                    "type": [
                        "Repository"
                    ],
                    "note": "Repository of source code and docker file."
                },
                {
                    "url": "http://computproteomics.bmb.sdu.dk:8192/app_direct/VIQoR/",
                    "type": [
                        "Service"
                    ],
                    "note": null
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            "download": [
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            ],
            "credit": [
                {
                    "name": "Vasileios Tsiamis",
                    "email": "vasileios@bmb.sdu.dk",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-1359-5253",
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                },
                {
                    "name": "Veit Schwämmle",
                    "email": "veits@bmb.sdu.dk",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-9708-6722",
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            "name": "3DRS",
            "description": "3DRS, a web-based tool to share interactive representations of 3D biomolecular structures and Molecular Dynamics trajectories",
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                            "uri": "http://edamontology.org/operation_0570",
                            "term": "Structure visualisation"
                        },
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                            "uri": "http://edamontology.org/operation_3890",
                            "term": "Trajectory visualization"
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                    ],
                    "input": [
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                            "data": {
                                "uri": "http://edamontology.org/data_1460",
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                                "uri": "http://edamontology.org/data_1459",
                                "term": "Nucleic acid structure"
                            },
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                                "term": "Trajectory data"
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                                    "uri": "http://edamontology.org/format_3650",
                                    "term": "netCDF"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3885",
                                    "term": "BinPos"
                                },
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                                    "uri": "http://edamontology.org/format_3875",
                                    "term": "XTC"
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                                    "uri": "http://edamontology.org/format_3910",
                                    "term": "trr"
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                    ],
                    "note": "Generate animated figures for macromolecular 3D structures and trajectories using NGL viewer",
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            ],
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                "PHP"
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                "BioExcel"
            ],
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                "Interoperability"
            ],
            "elixirNode": [
                "Spain"
            ],
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                "3D-BioInfo"
            ],
            "link": [
                {
                    "url": "https://mmb.irbbarcelona.org/3dRS/",
                    "type": [
                        "Service"
                    ],
                    "note": "Main web server"
                },
                {
                    "url": "https://github.com/gbayarri?tab=repositories&q=3drs",
                    "type": [
                        "Repository"
                    ],
                    "note": "GitHub repositories for the project"
                },
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                    "url": "https://3drs-documentation.readthedocs.io/en/latest/",
                    "type": [
                        "Other"
                    ],
                    "note": "Documentation in Read The Docs"
                }
            ],
            "download": [
                {
                    "url": "https://mmb.irbbarcelona.org/3dRS/",
                    "type": "Other",
                    "note": "Main Web Site",
                    "version": "1.0"
                }
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            "publication": [],
            "credit": [
                {
                    "name": "Adam Hospital",
                    "email": "adam.hospital@irbbarcelona.org",
                    "url": "https://www.irbbarcelona.org/en/research/adam-hospital",
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        },
        {
            "name": "CaverDock",
            "description": "Performs rapid analysis of transport processes in proteins. It models the transportation of a ligand from outside environment into the protein active or binding site and vice versa. It implements a novel algorithm to produce contiguous ligand trajectory and estimation of a binding energy along the pathway. The current version uses CAVER for pathway identification and heavily modified Autodock Vina as a docking engine.",
            "homepage": "https://loschmidt.chemi.muni.cz/caverdock/",
            "biotoolsID": "caverdock",
            "biotoolsCURIE": "biotools:caverdock",
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                "1.1"
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                    "operation": [
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                            "uri": "http://edamontology.org/operation_0482",
                            "term": "Protein-ligand docking"
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                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1460",
                                "term": "Protein structure"
                            },
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                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
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                        {
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                                "term": "Small molecule structure"
                            },
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                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1537",
                                "term": "Protein structure report"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1957",
                                    "term": "raw"
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                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        }
                    ],
                    "note": "trajectory of ligand passing through protein tunnel and its energy",
                    "cmd": null
                }
            ],
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                "Command-line tool"
            ],
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                {
                    "uri": "http://edamontology.org/topic_2814",
                    "term": "Protein structure analysis"
                },
                {
                    "uri": "http://edamontology.org/topic_0154",
                    "term": "Small molecules"
                },
                {
                    "uri": "http://edamontology.org/topic_0078",
                    "term": "Proteins"
                }
            ],
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                "Linux",
                "Windows",
                "Mac"
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                "Python"
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                "CAVER",
                "ELIXIR-CZ"
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                "Czech Republic"
            ],
            "elixirCommunity": [
                "3D-BioInfo"
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            "link": [],
            "download": [
                {
                    "url": "https://www.fi.muni.cz/~xfilipov/caverdock/caverdock-ubuntu-14.04.tar.gz",
                    "type": "Binaries",
                    "note": "v1.0, Ubuntu 14.04",
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                },
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                {
                    "doi": "10.1093/bioinformatics/btz386",
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                        "Primary"
                    ],
                    "version": "1.0",
                    "note": null,
                    "metadata": {
                        "title": "CaverDock: A molecular docking-based tool to analyse ligand transport through protein tunnels and channels",
                        "abstract": "© 2019 The Author(s).Motivation: Protein tunnels and channels are key transport pathways that allow ligands to pass between proteins' external and internal environments. These functionally important structural features warrant detailed attention. It is difficult to study the ligand binding and unbinding processes experimentally, while molecular dynamics simulations can be time-consuming and computationally demanding. Results: CaverDock is a new software tool for analysing the ligand passage through the biomolecules. The method uses the optimized docking algorithm of AutoDock Vina for ligand placement docking and implements a parallel heuristic algorithm to search the space of possible trajectories. The duration of the simulations takes from minutes to a few hours. Here we describe the implementation of the method and demonstrate CaverDock's usability by: (i) comparison of the results with other available tools, (ii) determination of the robustness with large ensembles of ligands and (iii) the analysis and comparison of the ligand trajectories in engineered tunnels. Thorough testing confirms that CaverDock is applicable for the fast analysis of ligand binding and unbinding in fundamental enzymology and protein engineering. Availability and implementation: User guide and binaries for Ubuntu are freely available for non-commercial use at https://loschmidt.chemi.muni.cz/caverdock/. The web implementation is available at https://loschmidt.chemi.muni.cz/caverweb/. The source code is available upon request. Supplementary information: Supplementary data are available at Bioinformatics online.",
                        "date": "2019-12-01T00:00:00Z",
                        "citationCount": 14,
                        "authors": [
                            {
                                "name": "Vavra O."
                            },
                            {
                                "name": "Filipovic J."
                            },
                            {
                                "name": "Plhak J."
                            },
                            {
                                "name": "Bednar D."
                            },
                            {
                                "name": "Marques S.M."
                            },
                            {
                                "name": "Brezovsky J."
                            },
                            {
                                "name": "Stourac J."
                            },
                            {
                                "name": "Matyska L."
                            },
                            {
                                "name": "Damborsky J."
                            }
                        ],
                        "journal": "Bioinformatics"
                    }
                },
                {
                    "doi": "10.1109/TCBB.2019.2907492",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": "1.0",
                    "note": null,
                    "metadata": {
                        "title": "CaverDock: A Novel Method for the Fast Analysis of Ligand Transport",
                        "abstract": "Here we present a novel method for the analysis of transport processes in proteins and its implementation called CaverDock. Our method is based on a modified molecular docking algorithm. It iteratively places the ligand along the access tunnel in such a way that the ligand movement is contiguous and the energy is minimized. The result of CaverDock calculation is a ligand trajectory and an energy profile of transport process. CaverDock uses the modified docking program Autodock Vina for molecular docking and implements a parallel heuristic algorithm for searching the space of possible trajectories. Our method lies in between the geometrical approaches and molecular dynamics simulations. Contrary to the geometrical methods, it provides an evaluation of chemical forces. However, it is far less computationally demanding and easier to set up compared to molecular dynamics simulations. CaverDock will find a broad use in the fields of computational enzymology, drug design, and protein engineering. The software is available free of charge to the academic users at https://loschmidt.chemi.muni.cz/caverdock/.",
                        "date": "2020-09-01T00:00:00Z",
                        "citationCount": 8,
                        "authors": [
                            {
                                "name": "Filipovic J."
                            },
                            {
                                "name": "Vavra O."
                            },
                            {
                                "name": "Plhak J."
                            },
                            {
                                "name": "Bednar D."
                            },
                            {
                                "name": "Marques S.M."
                            },
                            {
                                "name": "Brezovsky J."
                            },
                            {
                                "name": "Matyska L."
                            },
                            {
                                "name": "Damborsky J."
                            }
                        ],
                        "journal": "IEEE/ACM transactions on computational biology and bioinformatics"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Jiri Filipovic",
                    "email": "fila@mail.muni.cz",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-5703-9673",
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                        "Developer"
                    ],
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                },
                {
                    "name": "Ondrej Vavra",
                    "email": "o.vavra@mail.muni.cz",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
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                    "typeRole": [
                        "Contributor"
                    ],
                    "note": null
                },
                {
                    "name": "Jan Plhak",
                    "email": "408420@mail.muni.cz",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Developer"
                    ],
                    "note": null
                },
                {
                    "name": "David Bednar",
                    "email": "222755@mail.muni.cz",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-6803-0340",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
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                        "Contributor"
                    ],
                    "note": null
                },
                {
                    "name": "Sergio Marques",
                    "email": "smar96@gmail.com",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0002-6281-7505",
                    "gridid": null,
                    "rorid": null,
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                    "typeRole": [
                        "Contributor"
                    ],
                    "note": null
                },
                {
                    "name": "Jan Brezovsky",
                    "email": "brezovsky@mail.muni.cz",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0001-9677-5078",
                    "gridid": null,
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                },
                {
                    "name": "Jan Stourac",
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                    "url": null,
                    "orcidid": "https://orcid.org/0000-0003-3139-3700",
                    "gridid": null,
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                        "Support"
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                {
                    "name": "Ludek Matyska",
                    "email": "Ludek.Matyska@muni.cz",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0001-6399-5453",
                    "gridid": null,
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                    "name": "Jiri Damborsky",
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                    "name": "Masaryk University, Brno, Czech Republic",
                    "email": null,
                    "url": "https://www.muni.cz/",
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                },
                {
                    "name": "International Centre for Clinical Research, Brno, Czech Republic",
                    "email": null,
                    "url": "https://www.fnusa-icrc.org/en/",
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                },
                {
                    "name": "CaverDock team",
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                    "name": "European Commission",
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                    "typeEntity": "Funding agency",
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                    "name": "Czech Science Foundation",
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                {
                    "name": "Brno City Municipality",
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                    "typeEntity": "Funding agency",
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                }
            ],
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            "owner": "Loschmidt Laboratories",
            "additionDate": "2018-04-06T08:55:47Z",
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        },
        {
            "name": "PredictSNP2",
            "description": "A consensus classifier that combines five of the top performing tools (CADD, DANN, FATHMM, FunSeq2 and GWAVA) for the evaluation of pathogenic effect of SNPs within the human genome. The obtained results are provided together with annotations extracted from dbSNP, GenBank, Clinvar, OMIM, RegulomeDB, HaploReg, UCSC and Ensembl databases.",
            "homepage": "https://loschmidt.chemi.muni.cz/predictsnp2",
            "biotoolsID": "predictsnp2",
            "biotoolsCURIE": "biotools:predictsnp2",
            "version": [
                "1.0"
            ],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_3672",
                            "term": "Gene functional annotation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3225",
                            "term": "Variant classification"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_3498",
                                "term": "Sequence variations"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3019",
                                    "term": "GVF"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3016",
                                    "term": "VCF"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_3498",
                                "term": "Sequence variations"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3016",
                                    "term": "VCF"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3508",
                                    "term": "PDF"
                                }
                            ]
                        }
                    ],
                    "note": "VCF file containing scores and PDF file containing scores and database links",
                    "cmd": null
                }
            ],
            "toolType": [
                "Web application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_3063",
                    "term": "Medical informatics"
                },
                {
                    "uri": "http://edamontology.org/topic_2533",
                    "term": "DNA mutation"
                },
                {
                    "uri": "http://edamontology.org/topic_3325",
                    "term": "Rare diseases"
                },
                {
                    "uri": "http://edamontology.org/topic_0622",
                    "term": "Genomics"
                }
            ],
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "language": [
                "JavaScript",
                "Java"
            ],
            "license": "Proprietary",
            "collectionID": [
                "Czech Republic",
                "Rare Disease",
                "ELIXIR-CZ"
            ],
            "maturity": "Mature",
            "cost": "Free of charge (with restrictions)",
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                "Tools"
            ],
            "elixirNode": [
                "Czech Republic"
            ],
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            "link": [],
            "download": [
                {
                    "url": "https://loschmidt.chemi.muni.cz/peg/software/predictsnp2-standalone/",
                    "type": "Downloads page",
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                    "version": "1.0"
                }
            ],
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                {
                    "url": "https://loschmidt.chemi.muni.cz/predictsnp2/docs/userguide.pdf",
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                }
            ],
            "publication": [
                {
                    "doi": "10.1371/journal.pcbi.1004962",
                    "pmid": null,
                    "pmcid": null,
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                    "version": "1.0",
                    "note": null,
                    "metadata": {
                        "title": "PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions",
                        "abstract": "© 2016 Bendl et al.An important message taken from human genome sequencing projects is that the human population exhibits approximately 99.9% genetic similarity. Variations in the remaining parts of the genome determine our identity, trace our history and reveal our heritage. The precise delineation of phenotypically causal variants plays a key role in providing accurate personalized diagnosis, prognosis, and treatment of inherited diseases. Several computational methods for achieving such delineation have been reported recently. However, their ability to pinpoint potentially deleterious variants is limited by the fact that their mechanisms of prediction do not account for the existence of different categories of variants. Consequently, their output is biased towards the variant categories that are most strongly represented in the variant databases. Moreover, most such methods provide numeric scores but not binary predictions of the deleteriousness of variants or confidence scores that would be more easily understood by users. We have constructed three datasets covering different types of disease-related variants, which were divided across five categories: (i) regulatory, (ii) splicing, (iii) missense, (iv) synonymous, and (v) nonsense variants. These datasets were used to develop category-optimal decision thresholds and to evaluate six tools for variant prioritization: CADD, DANN, FATHMM, FitCons, FunSeq2 and GWAVA. This evaluation revealed some important advantages of the category-based approach. The results obtained with the five best-performing tools were then combined into a consensus score. Additional comparative analyses showed that in the case of missense variations, protein-based predictors perform better than DNA sequence-based predictors. A user-friendly web interface was developed that provides easy access to the five tools’ predictions, and their consensus scores, in a user-understandable format tailored to the specific features of different categories of variations. To enable comprehensive evaluation of variants, the predictions are complemented with annotations from eight databases. The web server is freely available to the community at http://loschmidt.chemi.muni.cz/predictsnp2.",
                        "date": "2016-05-01T00:00:00Z",
                        "citationCount": 78,
                        "authors": [
                            {
                                "name": "Bendl J."
                            },
                            {
                                "name": "Musil M."
                            },
                            {
                                "name": "Stourac J."
                            },
                            {
                                "name": "Zendulka J."
                            },
                            {
                                "name": "Damborsky J."
                            },
                            {
                                "name": "Brezovsky J."
                            }
                        ],
                        "journal": "PLoS Computational Biology"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Jaroslav Bendl",
                    "email": "jaroslav.bendl@gmail.com",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0001-9989-2720",
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                    "name": "Milos Musil",
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                },
                {
                    "name": "Jan Brezovsky",
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                    "url": null,
                    "orcidid": "https://orcid.org/0000-0001-9677-5078",
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                },
                {
                    "name": "Jiri Damborsky",
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                        "Contributor"
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                },
                {
                    "name": "Eric D. Wieben",
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                    "typeEntity": "Person",
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                    ],
                    "note": null
                },
                {
                    "name": "Jaroslav Zendulka",
                    "email": "zendulka@fit.vut.cz",
                    "url": null,
                    "orcidid": "https://orcid.org/0000-0001-8718-7493",
                    "gridid": null,
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                        "Contributor"
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                },
                {
                    "name": "Antonin Pavelka",
                    "email": "99207@mail.muni.cz",
                    "url": null,
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                    ],
                    "note": null
                },
                {
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                    "url": "https://loschmidt.chemi.muni.cz/peg/",
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                },
                {
                    "name": "Masaryk University, Brno, Czech Republic",
                    "email": null,
                    "url": "https://www.muni.cz/",
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