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{
    "count": 132,
    "next": "?page=2",
    "previous": null,
    "list": [
        {
            "name": "HMMER3",
            "description": "This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.",
            "homepage": "http://hmmer.org/",
            "biotoolsID": "hmmer3",
            "biotoolsCURIE": "biotools:hmmer3",
            "version": [
                "3.1b1"
            ],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0335",
                            "term": "Formatting"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": []
                        }
                    ],
                    "note": "alimask is used to apply a mask line to a multiple sequence alignment, based on provided alignment or model coordinates.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0492",
                            "term": "Multiple sequence alignment"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0850",
                                "term": "Sequence set"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1916",
                                "term": "Alignment"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1961",
                                    "term": "Stockholm format"
                                }
                            ]
                        }
                    ],
                    "note": "Align sequences to a profile HMM The < hmmfile > should contain only a single profile.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0296",
                            "term": "Sequence profile generation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "note": "Construct profile HMM(s) from multiple sequence alignment(s).",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0336",
                            "term": "Format validation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3434",
                            "term": "Conversion"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1370",
                                    "term": "HMMER format"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3329",
                                    "term": "HMMER3"
                                }
                            ]
                        }
                    ],
                    "note": "The hmmconvert utility converts an input profile file to different HMMER formats.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0230",
                            "term": "Sequence generation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2044",
                                "term": "Sequence"
                            },
                            "format": []
                        }
                    ],
                    "note": "Sample sequences from a profile HMM.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2422",
                            "term": "Data retrieval"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0968",
                                "term": "Keyword"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "note": "Retrieve profile HMM(s) from a file.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2238",
                            "term": "Statistical calculation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1361",
                                "term": "Position frequency matrix"
                            },
                            "format": []
                        }
                    ],
                    "note": "Given an HMM, produce data required to build an HMM logo.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": "Daemon for searching a protein query against a protein database.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0335",
                            "term": "Formatting"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3329",
                                    "term": "HMMER3"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2048",
                                "term": "Report"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0955",
                                "term": "Data index"
                            },
                            "format": []
                        }
                    ],
                    "note": "Prepare an HMM database for hmmscan.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1927",
                                    "term": "EMBL format"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1936",
                                    "term": "GenBank format"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1963",
                                    "term": "UniProtKB format"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0957",
                                "term": "Database metadata"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2080",
                                "term": "Database search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Search protein sequence(s) against a protein profile database. query sequence to search the target database of profiles Needs to have those four auxiliary binary files generated by hmmpress. The output format is designed to be human-readable, but is often so voluminous that reading it is impractical.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0850",
                                "term": "Sequence set"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2080",
                                "term": "Database search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Search profile(s) against a sequence database. Query profile to search the target database of sequences. Sequence database. Ranked lists of the sequences with the most significant matches to the profile.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_3481",
                            "term": "Probabilistic sequence generation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2238",
                            "term": "Statistical calculation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2048",
                                "term": "Report"
                            },
                            "format": []
                        }
                    ],
                    "note": "Collect score distributions on random sequences. The output is a table of numbers, one row for each model. Four different parametric fits to the score data are tested: (1) maximum likelihood fits to both location (mu/tau) and slope (lambda) parameters; (2) assuming lambda=log 2, maximum likelihood fit to the location parameter only; (3) same but assuming an edge- corrected lambda, using current procedures in H3 [Eddy, 2008]; and (4) using both parameters determined by H3s current procedures.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2238",
                            "term": "Statistical calculation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2048",
                                "term": "Report"
                            },
                            "format": []
                        }
                    ],
                    "note": "Display summary statistics for a profile file. Tabular file of summary statistics for each profile.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0338",
                            "term": "Sequence database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1233",
                                "term": "Sequence set (protein)"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0857",
                                "term": "Sequence search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Iteratively search sequence(s) against a protein database. database sequence The output format is designed to be human-readable, but is often so voluminous that reading it is impractical.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0335",
                            "term": "Formatting"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_3494",
                                "term": "DNA sequence"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2044",
                                "term": "Sequence"
                            },
                            "format": []
                        }
                    ],
                    "note": "Build a HMMER binary database file from a sequence file. This binary file may be used as a target database for the DNA search tool nhmmer.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0338",
                            "term": "Sequence database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2977",
                                "term": "Nucleic acid sequence"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1234",
                                "term": "Sequence set (nucleic acid)"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0857",
                                "term": "Sequence search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Search DNA/RNA queries against a DNA/RNA sequence database. nucleic sequence database",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2977",
                                "term": "Nucleic acid sequence"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2080",
                                "term": "Database search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Search nucleotide sequence(s) against collections of nucleotide profiles. The <hmmdb> needs to be pressed using hmmpress before it can be searched with hmmscan. The output format is designed to be human-readable, but is often so voluminous that reading it is impractical.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0338",
                            "term": "Sequence database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1233",
                                "term": "Sequence set (protein)"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0857",
                                "term": "Sequence search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Search protein sequence(s) against a protein sequence database. database of sequences Ranked lists of the sequences with the most significant matches to the query. The output format is designed to be human-readable, but is often so voluminous that reading it is impractical.",
                    "cmd": null
                }
            ],
            "toolType": [
                "Command-line tool",
                "Web application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
                },
                {
                    "uri": "http://edamontology.org/topic_0160",
                    "term": "Sequence sites, features and motifs"
                },
                {
                    "uri": "http://edamontology.org/topic_0623",
                    "term": "Gene and protein families"
                }
            ],
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "language": [
                "Perl",
                "C"
            ],
            "license": "Other",
            "collectionID": [
                "HMMER",
                "Animal and Crop Genomics"
            ],
            "maturity": null,
            "cost": null,
            "accessibility": null,
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://github.com/EddyRivasLab/hmmer",
                    "type": [
                        "Repository"
                    ],
                    "note": null
                },
                {
                    "url": "https://github.com/EddyRivasLab/hmmer/issues",
                    "type": [
                        "Issue tracker"
                    ],
                    "note": null
                }
            ],
            "download": [],
            "documentation": [
                {
                    "url": "http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf",
                    "type": [
                        "User manual"
                    ],
                    "note": "HMMER User Guide"
                },
                {
                    "url": "http://hmmer.org/documentation.html",
                    "type": [
                        "General"
                    ],
                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1093/nar/gkr367",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "HMMER web server: Interactive sequence similarity searching",
                        "abstract": "HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them. © 2011 The Author(s).",
                        "date": "2011-07-01T00:00:00Z",
                        "citationCount": 2484,
                        "authors": [
                            {
                                "name": "Finn R.D."
                            },
                            {
                                "name": "Clements J."
                            },
                            {
                                "name": "Eddy S.R."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                },
                {
                    "doi": "10.1371/journal.pcbi.1002195",
                    "pmid": "22039361",
                    "pmcid": "PMC3197634",
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "Accelerated profile HMM searches",
                        "abstract": "Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the \"multiple segment Viterbi\" (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call \"sparse rescaling\". These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches. © 2011 Sean R. Eddy.",
                        "date": "2011-10-01T00:00:00Z",
                        "citationCount": 2414,
                        "authors": [
                            {
                                "name": "Eddy S.R."
                            }
                        ],
                        "journal": "PLoS Computational Biology"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Sean Eddy",
                    "email": "sean@eddylab.org",
                    "url": null,
                    "orcidid": "http://orcid.org/0000-0001-6676-4706",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Primary contact"
                    ],
                    "note": null
                }
            ],
            "community": {
                "biolib": {
                    "app_name": "hmmsearch",
                    "author_name": "HMMER",
                    "author_username": "HMMER"
                }
            },
            "owner": "ELIXIR-FR",
            "additionDate": "2015-04-03T13:17:38Z",
            "lastUpdate": "2021-10-15T14:09:31.104633Z",
            "editPermission": {
                "type": "group",
                "authors": [
                    "animalandcropgenomics",
                    "laurasansc"
                ]
            },
            "validated": 1,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": null
        },
        {
            "name": "IPC",
            "description": "Web service and standalone program for the estimation of protein and peptide pI using different sets of dissociation constant (pKa) values, including computationally optimized pKa sets. According to the benchmarks, the newly developed pKa sets outperform previous algorithms by at least 14.9 % for proteins and 0.9 % for peptides (on average, 22.1 % and 59.6 %, respectively), which corresponds to an average error of the pI estimation of 0.87 and 0.25 pH units, respectively.",
            "homepage": "http://isoelectric.org",
            "biotoolsID": "ipc",
            "biotoolsCURIE": "biotools:ipc",
            "version": [
                "1.0"
            ],
            "otherID": [],
            "relation": [
                {
                    "biotoolsID": "ipc_2.0",
                    "type": "hasNewVersion"
                },
                {
                    "biotoolsID": "proteome-pi_2.0",
                    "type": "usedBy"
                },
                {
                    "biotoolsID": "proteome-pi",
                    "type": "usedBy"
                }
            ],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0250",
                            "term": "Protein property calculation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1528",
                                "term": "Protein isoelectric point"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_2330",
                                    "term": "Textual format"
                                }
                            ]
                        }
                    ],
                    "note": "Isoelectric point, molecular weight",
                    "cmd": null
                }
            ],
            "toolType": [
                "Command-line tool",
                "Web service"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0123",
                    "term": "Protein properties"
                },
                {
                    "uri": "http://edamontology.org/topic_3520",
                    "term": "Proteomics experiment"
                },
                {
                    "uri": "http://edamontology.org/topic_3047",
                    "term": "Molecular biology"
                },
                {
                    "uri": "http://edamontology.org/topic_3292",
                    "term": "Biochemistry"
                },
                {
                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
                }
            ],
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "language": [
                "Python"
            ],
            "license": "Other",
            "collectionID": [
                "Proteomics"
            ],
            "maturity": "Mature",
            "cost": "Free of charge (with restrictions)",
            "accessibility": null,
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [],
            "download": [
                {
                    "url": "http://isoelectric.org/ipc-1.0.zip",
                    "type": "Software package",
                    "note": null,
                    "version": null
                }
            ],
            "documentation": [
                {
                    "url": "http://isoelectric.org/algorithms.html",
                    "type": [
                        "General"
                    ],
                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1186/s13062-016-0159-9",
                    "pmid": "27769290",
                    "pmcid": "PMC5075173",
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "IPC - Isoelectric Point Calculator",
                        "abstract": "© 2016 The Author(s).Background: Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Additionally, pI estimation can be helpful during protein crystallization trials. Results: Here, I present the Isoelectric Point Calculator (IPC), a web service and a standalone program for the accurate estimation of protein and peptide pI using different sets of dissociation constant (pKa) values, including two new computationally optimized pKa sets. According to the presented benchmarks, the newly developed IPC pKa sets outperform previous algorithms by at least 14.9 % for proteins and 0.9 % for peptides (on average, 22.1 % and 59.6 %, respectively), which corresponds to an average error of the pI estimation equal to 0.87 and 0.25 pH units for proteins and peptides, respectively. Moreover, the prediction of pI using the IPC pKa's leads to fewer outliers, i.e., predictions affected by errors greater than a given threshold. Conclusions: The IPC service is freely available at http://isoelectric.ovh.org Peptide and protein datasets used in the study and the precalculated pI for the PDB and some of the most frequently used proteomes are available for large-scale analysis and future development. Reviewers: This article was reviewed by Frank Eisenhaber and Zoltán Gáspári",
                        "date": "2016-10-21T00:00:00Z",
                        "citationCount": 163,
                        "authors": [
                            {
                                "name": "Kozlowski L.P."
                            }
                        ],
                        "journal": "Biology Direct"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Lukasz Kozlowski",
                    "email": "lukasz.kozlowski.lpk@gmail.com",
                    "url": "http://bioinformatics.netmark.pl",
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                    ],
                    "note": null
                }
            ],
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            "owner": "lukaskoz",
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            },
            "validated": 1,
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            "confidence_flag": null
        },
        {
            "name": "XPlatCom (Cross PLATform COMmander)",
            "description": "It facilitates several steps that frequently occur in the context of multi-OMICS workflows like data conversion, quality control, data comparison, differential/statistical analyses, GO and pathway analyses. In the present version, CrossPlatformCommander enables Integration data obtained from Proteomics and Transcriptomics measurements.",
            "homepage": "https://www.ruhr-uni-bochum.de/mpc/software/legacy/index.html.en#XPlatCom",
            "biotoolsID": "xplatcom",
            "biotoolsCURIE": "biotools:xplatcom",
            "version": [
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            ],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2997",
                            "term": "Protein comparison"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2998",
                            "term": "Nucleic acid comparison"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3659",
                            "term": "Regression analysis"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0928",
                                "term": "Gene expression profile"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1638",
                                    "term": "cel"
                                },
                                {
                                    "uri": "http://edamontology.org/format_2330",
                                    "term": "Textual format"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3578",
                                    "term": "IDAT"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2536",
                                "term": "Mass spectrometry data"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3244",
                                    "term": "mzML"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1277",
                                "term": "Protein features"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3764",
                                    "term": "idXML"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1449",
                                "term": "Comparison matrix (amino acid)"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3752",
                                    "term": "CSV"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2884",
                                "term": "Plot"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3603",
                                    "term": "PNG"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1448",
                                "term": "Comparison matrix (nucleotide)"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3752",
                                    "term": "CSV"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_3754",
                                "term": "GO-term enrichment data"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3752",
                                    "term": "CSV"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3603",
                                    "term": "PNG"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3508",
                                    "term": "PDF"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2343",
                                "term": "Pathway ID (KEGG)"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_2332",
                                    "term": "XML"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3752",
                                    "term": "CSV"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2600",
                                "term": "Pathway or network"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3603",
                                    "term": "PNG"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2048",
                                "term": "Report"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3508",
                                    "term": "PDF"
                                }
                            ]
                        }
                    ],
                    "note": "Calculation and visualization of correlation between quantitative data arising from different omics platforms. The software imports quantitative expression profiles of currently two biomolecule entities (i.e. quantitative Transcriptomics (mRNA) and Proteomics expression data).\nThe output contains also the result of GO and pathway analysis for both omics platforms. Integrative analysis gives a scatter plot (and linear regression) of the corresponding Transcriptomics and Proteomics expression profiles.",
                    "cmd": null
                }
            ],
            "toolType": [
                "Desktop application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_3391",
                    "term": "Omics"
                }
            ],
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "language": [
                "Java"
            ],
            "license": null,
            "collectionID": [
                "de.NBI",
                "BioInfra.Prot"
            ],
            "maturity": "Legacy",
            "cost": "Free of charge",
            "accessibility": null,
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            "download": [],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.1016/j.bbapap.2013.02.029",
                    "pmid": "23501674",
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": null
                }
            ],
            "credit": [
                {
                    "name": "PD Dr. Martin Eisenacher",
                    "email": "martin.eisenacher@rub.de",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Primary contact"
                    ],
                    "note": "If contacting use \"SPARROW\" to avoid spam deluge."
                },
                {
                    "name": "Dr. Michael Kohl",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": null,
                    "typeRole": [
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                    ],
                    "note": null
                }
            ],
            "community": null,
            "owner": "BioInfra.Prot",
            "additionDate": "2016-01-19T16:45:50Z",
            "lastUpdate": "2021-08-31T09:10:13Z",
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            },
            "validated": 1,
            "homepage_status": 0,
            "elixir_badge": 0,
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        },
        {
            "name": "ProLiC (Protein List Comparator)",
            "description": "It includes adresses the problem of protein list comparison, which can be challenging due to different or changing database accession numbers.\nIn addition to a simple accession based comparison, ProLiC permits a more reliable comparison of an arbitrary number of protein lists by considering measured sequence and/or peptide information.",
            "homepage": "https://www.ruhr-uni-bochum.de/mpc/software/legacy/index.html.de#ProLiC",
            "biotoolsID": "prolic",
            "biotoolsCURIE": "biotools:prolic",
            "version": [
                "1"
            ],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2997",
                            "term": "Protein comparison"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3475",
                                    "term": "TSV"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0850",
                                "term": "Sequence set"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3475",
                                    "term": "TSV"
                                }
                            ]
                        }
                    ],
                    "note": "ProLiC includes different possibilities to solve the problem of protein list comparison. \nProLiC uses its own data format (tsv or csv files) containing protein accessions as well as protein and peptide sequences. However in the medium run support of standard format is intended. The result of a ProLiC protein list comparison is a single text file, which gives the calculated overlaps and set differences in a very simple way.",
                    "cmd": null
                }
            ],
            "toolType": [
                "Command-line tool"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
                }
            ],
            "operatingSystem": [
                "Linux"
            ],
            "language": [],
            "license": null,
            "collectionID": [
                "de.NBI",
                "Proteomics",
                "BioInfra.Prot"
            ],
            "maturity": "Legacy",
            "cost": "Free of charge",
            "accessibility": null,
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                    "pmid": null,
                    "pmcid": null,
                    "type": [
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                    ],
                    "version": null,
                    "note": null,
                    "metadata": null
                }
            ],
            "credit": [
                {
                    "name": "PD Dr. Martin Eisenacher",
                    "email": "martin.eisenacher@rub.de",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Primary contact"
                    ],
                    "note": "If contacting use \"SPARROW\" in subject due to spam deluge."
                },
                {
                    "name": "Dr. Michael Kohl",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
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                    "fundrefid": null,
                    "typeEntity": "Person",
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            ],
            "community": null,
            "owner": "BioInfra.Prot",
            "additionDate": "2016-05-11T10:00:46Z",
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        },
        {
            "name": "GhostKOALA",
            "description": "GhostKOALA (KEGG Orthology And Links Annotation) is another service for annotating metagenomes and understanding ecosystems.",
            "homepage": "https://www.kegg.jp/ghostkoala/",
            "biotoolsID": "ghostkoala",
            "biotoolsCURIE": "biotools:ghostkoala",
            "version": [],
            "otherID": [],
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                {
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                        },
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0533",
                            "term": "Expression profile pathway mapping"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": [
                                {
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                                    "term": "FASTA"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0916",
                                "term": "Gene report"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1872",
                                "term": "Taxonomic classification"
                            },
                            "format": []
                        }
                    ],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Web application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0602",
                    "term": "Molecular interactions, pathways and networks"
                },
                {
                    "uri": "http://edamontology.org/topic_3174",
                    "term": "Metagenomics"
                },
                {
                    "uri": "http://edamontology.org/topic_3837",
                    "term": "Metagenomic sequencing"
                }
            ],
            "operatingSystem": [],
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            "link": [
                {
                    "url": "https://www.kegg.jp/feedback/?ans_category=Gene%20function%20annotation",
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                        "Helpdesk"
                    ],
                    "note": null
                }
            ],
            "download": [],
            "documentation": [
                {
                    "url": "https://www.kegg.jp/blastkoala/help_ghostkoala.html",
                    "type": [
                        "General"
                    ],
                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1016/j.jmb.2015.11.006",
                    "pmid": "26585406",
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences",
                        "abstract": "© 2015 The Authors.BlastKOALA and GhostKOALA are automatic annotation servers for genome and metagenome sequences, which perform KO (KEGG Orthology) assignments to characterize individual gene functions and reconstruct KEGG pathways, BRITE hierarchies and KEGG modules to infer high-level functions of the organism or the ecosystem. Both servers are made freely available at the KEGG Web site (http://www.kegg.jp/blastkoala/). In BlastKOALA, the KO assignment is performed by a modified version of the internally used KOALA algorithm after the BLAST search against a non-redundant dataset of pangenome sequences at the species, genus or family level, which is generated from the KEGG GENES database by retaining the KO content of each taxonomic category. In GhostKOALA, which utilizes more rapid GHOSTX for database search and is suitable for metagenome annotation, the pangenome dataset is supplemented with Cd-hit clusters including those for viral genes. The result files may be downloaded and manipulated for further KEGG Mapper analysis, such as comparative pathway analysis using multiple BlastKOALA results.",
                        "date": "2016-02-22T00:00:00Z",
                        "citationCount": 944,
                        "authors": [
                            {
                                "name": "Kanehisa M."
                            },
                            {
                                "name": "Sato Y."
                            },
                            {
                                "name": "Morishima K."
                            }
                        ],
                        "journal": "Journal of Molecular Biology"
                    }
                }
            ],
            "credit": [],
            "community": null,
            "owner": "Kigaard",
            "additionDate": "2021-05-26T20:01:14Z",
            "lastUpdate": "2021-06-04T13:42:01Z",
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                "type": "private",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": null
        },
        {
            "name": "Unipept",
            "description": "Metaproteomics data analysis with a focus on interactive data visualizations.",
            "homepage": "http://unipept.ugent.be/",
            "biotoolsID": "unipept",
            "biotoolsCURIE": "biotools:unipept",
            "version": [
                "3.1"
            ],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2423",
                            "term": "Prediction and recognition"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0337",
                            "term": "Visualisation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0850",
                                "term": "Sequence set"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0872",
                                "term": "Phylogenetic tree"
                            },
                            "format": []
                        }
                    ],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Workbench"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
                },
                {
                    "uri": "http://edamontology.org/topic_3922",
                    "term": "Proteogenomics"
                },
                {
                    "uri": "http://edamontology.org/topic_3050",
                    "term": "Biodiversity"
                },
                {
                    "uri": "http://edamontology.org/topic_0769",
                    "term": "Workflows"
                }
            ],
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "language": [],
            "license": "MIT",
            "collectionID": [
                "BIG N2N",
                "Proteomics",
                "UGent"
            ],
            "maturity": null,
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            "accessibility": null,
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            "elixirCommunity": [],
            "link": [],
            "download": [],
            "documentation": [
                {
                    "url": "https://unipept.ugent.be/apidocs",
                    "type": [
                        "API documentation"
                    ],
                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1093/bioinformatics/btw039",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "Unipept web services for metaproteomics analysis",
                        "abstract": "© 2016 The Author 2016. Published by Oxford University Press. All rights reserved.Summary Unipept is an open source web application that is designed for metaproteomics analysis with a focus on interactive datavisualization. It is underpinned by a fast index built from UniProtKB and the NCBI taxonomy that enables quick retrieval of all UniProt entries in which a given tryptic peptide occurs. Unipept version 2.4 introduced web services that provide programmatic access to the metaproteomics analysis features. This enables integration of Unipept functionality in custom applications and data processing pipelines. Availability and implementation: The web services are freely available at http://api.unipept.ugent.be and are open sourced under the MIT license. Supplementary information: Supplementary data are available at Bioinformatics online.",
                        "date": "2016-06-01T00:00:00Z",
                        "citationCount": 32,
                        "authors": [
                            {
                                "name": "Mesuere B."
                            },
                            {
                                "name": "Willems T."
                            },
                            {
                                "name": "Van Der Jeugt F."
                            },
                            {
                                "name": "Devreese B."
                            },
                            {
                                "name": "Vandamme P."
                            },
                            {
                                "name": "Dawyndt P."
                            }
                        ],
                        "journal": "Bioinformatics"
                    }
                },
                {
                    "doi": "10.1021/ACS.JPROTEOME.0C00855",
                    "pmid": "33401902",
                    "pmcid": null,
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "Unipept Desktop: A Faster, More Powerful Metaproteomics Results Analysis Tool",
                        "abstract": "© 2021 American Chemical Society.Metaproteomics has become an important research tool to study microbial systems, which has resulted in increased metaproteomics data generation. However, efficient tools for processing the acquired data have lagged behind. One widely used tool for metaproteomics data interpretation is Unipept, a web-based tool that provides, among others, interactive and insightful visualizations. Due to its web-based implementation, however, the Unipept web application is limited in the amount of data that can be analyzed. In this manuscript we therefore present Unipept Desktop, a desktop application version of Unipept that is designed to drastically increase the throughput and capacity of metaproteomics data analysis. Moreover, it provides a novel comparative analysis pipeline and improves the organization of experimental data into projects, thus addressing the growing need for more efficient and versatile analysis tools for metaproteomics data.",
                        "date": "2021-01-01T00:00:00Z",
                        "citationCount": 0,
                        "authors": [
                            {
                                "name": "Verschaffelt P."
                            },
                            {
                                "name": "Van Den Bossche T."
                            },
                            {
                                "name": "Martens L."
                            },
                            {
                                "name": "Dawyndt P."
                            },
                            {
                                "name": "Mesuere B."
                            }
                        ],
                        "journal": "Journal of Proteome Research"
                    }
                }
            ],
            "credit": [
                {
                    "name": "ugent.be",
                    "email": null,
                    "url": null,
                    "orcidid": null,
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                    "typeEntity": "Institute",
                    "typeRole": [
                        "Provider"
                    ],
                    "note": null
                },
                {
                    "name": null,
                    "email": "Unipept@ugent.be",
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
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                    "typeRole": [
                        "Primary contact"
                    ],
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                }
            ],
            "community": null,
            "owner": "bmesuere",
            "additionDate": "2016-05-17T10:18:37Z",
            "lastUpdate": "2021-05-27T07:31:15Z",
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                "authors": [
                    "proteomics.bio.tools"
                ]
            },
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            "confidence_flag": null
        },
        {
            "name": "EnzymeMiner",
            "description": "EnzymeMiner identifies putative members of enzyme families or subfamilies and facilitates the selection of promising targets for experimental characterization. Two key selection criteria are (i) the predicted solubility and (ii) the sequence identities visualised using an interactive sequence similarity network. The search query can be a sequence from the Swiss-Prot database or a custom sequence with a custom description of essential residues. The output is an interactive selection table containing annotated identified sequences.",
            "homepage": "https://loschmidt.chemi.muni.cz/enzymeminer/",
            "biotoolsID": "enzymeminer",
            "biotoolsCURIE": "biotools:enzymeminer",
            "version": [
                "1.0"
            ],
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            "relation": [
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                {
                    "biotoolsID": "usearch",
                    "type": "uses"
                },
                {
                    "biotoolsID": "clustalo",
                    "type": "uses"
                },
                {
                    "biotoolsID": "tmhmm",
                    "type": "uses"
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                    "biotoolsID": "interproscan_4",
                    "type": "uses"
                },
                {
                    "biotoolsID": "soluprot",
                    "type": "uses"
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                {
                    "biotoolsID": "bioproject",
                    "type": "uses"
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                {
                    "biotoolsID": "ncbi_taxonomy_database",
                    "type": "uses"
                },
                {
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                },
                {
                    "biotoolsID": "mmseqs2",
                    "type": "uses"
                },
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                }
            ],
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                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0346",
                            "term": "Sequence similarity search"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0291",
                            "term": "Sequence clustering"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0361",
                            "term": "Sequence annotation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0409",
                            "term": "Protein solubility prediction"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": [
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                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1277",
                                "term": "Protein features"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3620",
                                    "term": "xlsx"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1233",
                                "term": "Sequence set (protein)"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1245",
                                "term": "Sequence cluster (protein)"
                            },
                            "format": []
                        }
                    ],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Web application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
                },
                {
                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
                },
                {
                    "uri": "http://edamontology.org/topic_3473",
                    "term": "Data mining"
                },
                {
                    "uri": "http://edamontology.org/topic_0821",
                    "term": "Enzymes"
                },
                {
                    "uri": "http://edamontology.org/topic_0078",
                    "term": "Proteins"
                }
            ],
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "language": [
                "JavaScript",
                "Java"
            ],
            "license": "Proprietary",
            "collectionID": [
                "Czech Republic",
                "ELIXIR-CZ"
            ],
            "maturity": "Mature",
            "cost": "Free of charge (with restrictions)",
            "accessibility": "Open access",
            "elixirPlatform": [
                "Tools"
            ],
            "elixirNode": [
                "Czech Republic"
            ],
            "elixirCommunity": [],
            "link": [],
            "download": [],
            "documentation": [
                {
                    "url": "https://loschmidt.chemi.muni.cz/enzymeminer/help",
                    "type": [
                        "User manual"
                    ],
                    "note": null
                },
                {
                    "url": "https://loschmidt.chemi.muni.cz/enzymeminer/example",
                    "type": [
                        "Training material"
                    ],
                    "note": null
                },
                {
                    "url": "https://loschmidt.chemi.muni.cz/enzymeminer/terms-of-use",
                    "type": [
                        "Terms of use"
                    ],
                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1093/nar/gkaa372",
                    "pmid": null,
                    "pmcid": null,
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "EnzymeMiner: Automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities",
                        "abstract": "© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.Millions of protein sequences are being discovered at an incredible pace, representing an inexhaustible source of biocatalysts. Despite genomic databases growing exponentially, classical biochemical characterization techniques are time-demanding, cost-ineffective and low-throughput. Therefore, computational methods are being developed to explore the unmapped sequence space efficiently. Selection of putative enzymes for biochemical characterization based on rational and robust analysis of all available sequences remains an unsolved problem. To address this challenge, we have developed EnzymeMiner––a web server for automated screening and annotation of diverse family members that enables selection of hits for wet-lab experiments. EnzymeMiner prioritizes sequences that are more likely to preserve the catalytic activity and are heterologously expressible in a soluble form in Escherichia coli. The solubility prediction employs the in-house SoluProt predictor developed using machine learning. EnzymeMiner reduces the time devoted to data gathering, multi-step analysis, sequence prioritization and selection from days to hours. The successful use case for the haloalkane dehalogenase family is described in a comprehensive tutorial available on the EnzymeMiner web page. EnzymeMiner is a universal tool applicable to any enzyme family that provides an interactive and easy-to-use web interface freely available at https://loschmidt.chemi.muni.cz/enzymeminer/.",
                        "date": "2021-01-01T00:00:00Z",
                        "citationCount": 6,
                        "authors": [
                            {
                                "name": "Hon J."
                            },
                            {
                                "name": "Borko S."
                            },
                            {
                                "name": "Stourac J."
                            },
                            {
                                "name": "Prokop Z."
                            },
                            {
                                "name": "Zendulka J."
                            },
                            {
                                "name": "Bednar D."
                            },
                            {
                                "name": "Martinek T."
                            },
                            {
                                "name": "Damborsky J."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Jiri Hon",
                    "email": "xhonji01@stud.fit.vutbr.cz",
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                    "name": "Simeon Borko",
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                    "name": "Jan Stourac",
                    "email": "stourac.jan@gmail.com",
                    "url": null,
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                    "name": "Jaroslav Zendulka",
                    "email": "zendulka@fit.vut.cz",
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                    "name": "Tomas Martinek",
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                {
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                {
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                {
                    "biotoolsID": "i-tasser",
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                {
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                {
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                {
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            ],
            "function": [
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                        },
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                            "uri": "http://edamontology.org/operation_0244",
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                            "term": "Sequence alignment analysis (site correlation)"
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                            "term": "Protein secondary structure assignment"
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                            "uri": "http://edamontology.org/operation_3092",
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                                "term": "Protein report"
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                                    "term": "XML"
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                        },
                        {
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                                "term": "Protein structure report"
                            },
                            "format": [
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                                    "term": "Textual format"
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                        },
                        {
                            "data": {
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                                "term": "DNA sequence (raw)"
                            },
                            "format": [
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                                    "term": "HTML"
                                },
                                {
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                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0872",
                                "term": "Phylogenetic tree"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1910",
                                    "term": "newick"
                                }
                            ]
                        }
                    ],
                    "note": "pockets and tunnels, back translated sequence with degenerated codons",
                    "cmd": null
                },
                {
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                            "uri": "http://edamontology.org/operation_0482",
                            "term": "Protein-ligand docking"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1463",
                                "term": "Small molecule structure"
                            },
                            "format": [
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                                    "term": "PDB"
                                },
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                                    "term": "SMILES"
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                        }
                    ],
                    "output": [
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