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GET /api/t/?format=api&inputDataTypeID=%22data_2976%22
{ "count": 292, "next": "?page=2", "previous": null, "list": [ { "name": "Life Science Protein File Audit", "description": "Offline, deterministic bioinformatics command-line tool for auditing protein FASTA sequences and PDB coordinate files. Analyzes amino-acid composition and ambiguous residues in FASTA files, and inventories observed C-alpha residues in the first PDB model. Produces structured JSON reports with source SHA-256 digests and bounded quality warnings. Supports reproducible execution and CWL workflow integration. 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For the archived 0.4.0 release, use Zenodo DOI 10.5281/zenodo.23447089", "version": "main" } ], "documentation": [ { "url": "https://github.com/lostlight530/life-science-ecosystem-lab/blob/main/bio_tool/README.md", "type": [ "User manual" ], "note": "Installation, ls-bio protein-fasta and protein-pdb commands, supported inputs, bounded JSON outputs, 8 MB input limit, CWL wrappers and stated limitations" } ], "publication": [ { "doi": "10.5281/zenodo.23447088", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": "Software archive (Zenodo concept DOI) for citing the tool; not a peer-reviewed article", "metadata": null } ], "credit": [ { "name": "Xuanyi Jiang", "email": "lostlight520@gmail.com", "url": "https://github.com/lostlight530/life-science-ecosystem-lab", "orcidid": "https://orcid.org/0009-0001-3617-0832", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer", "Provider", "Support", "Documentor", "Contributor" ], "note": "Designed and implemented a deterministic command-line audit for protein FASTA and PDB files, including amino-acid composition analysis, ambiguous-residue reporting, first-model C-alpha residue inventory, source SHA-256 reporting, bounded quality warnings, and reproducibility-oriented testing and documentation" } ], "owner": "user.1791708261", "additionDate": "2026-10-17T14:35:25.534070Z", "lastUpdate": "2026-10-18T12:21:34.788307Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "peptide-mass (Peptide.Express)", "description": "Command-line and Python library (PyPI: peptide-mass) that computes monoisotopic and average molecular masses and ESI [M+nH]n+ m/z values for peptide amino-acid sequences. 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"confidence_flag": null }, { "name": "HSYMDOCK", "description": "Symmetric protein docking for oligomers with Cn or Dn symmetry from the structure or sequence of a subunit molecule.", "homepage": "http://huanglab.phys.hust.edu.cn/hsymdock/", "biotoolsID": "hsymdock", "biotoolsCURIE": "biotools:hsymdock", "version": [ "2018-06-02" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0478", "term": "Molecular docking" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_2200", "term": "FASTA-like (text)" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "PHP" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://huanglab.phys.hust.edu.cn/hsymdock/help.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gky398", "pmid": "29846641", "pmcid": "PMC6030965", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "HSYMDOCK: A docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry", "abstract": "A major subclass of protein-protein interactions is formed by homo-oligomers with certain symmetry. Therefore, computational modeling of the symmetric protein complexes is important for understanding the molecular mechanism of related biological processes. Although several symmetric docking algorithms have been developed for Cn symmetry, few docking servers have been proposed for Dn symmetry. Here, we present HSYMDOCK, a web server of our hierarchical symmetric docking algorithm that supports both Cn and Dn symmetry. The HSYMDOCK server was extensively evaluated on three benchmarks of symmetric protein complexes, including the 20 CASP11-CAPRI30 homo-oligomer targets, the symmetric docking benchmark of 213 Cn targets and 35 Dn targets, and a nonredundant test set of 55 transmembrane proteins. It was shown that HSYMDOCK obtained a significantly better performance than other similar docking algorithms. The server supports both sequence and structure inputs for the monomer/subunit. Users have an option to provide the symmetry type of the complex, or the server can predict the symmetry type automatically. The docking process is fast and on average consumes 101/420 min for a docking job. The HSYMDOCK web server is available at http://huanglab.phys.hust.edu.cn/hsymdock/.", "date": "2018-07-02T00:00:00Z", "citationCount": 33, "authors": [ { "name": "Yan Y." }, { "name": "Tao H." }, { "name": "Huang S.-Y." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": null, "email": "huanglab@hust.edu.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-06-18T09:30:36Z", "lastUpdate": "2024-11-25T14:41:44.638481Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MobiDB-lite", "description": "MobiDB-lite is an optimized method for highly specific predictions of long intrinsically disordered regions", "homepage": "http://protein.bio.unipd.it/mobidblite/", "biotoolsID": "mobidb-lite", "biotoolsCURIE": "biotools:mobidb-lite", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" }, { "uri": "http://edamontology.org/operation_2480", "term": "Structure analysis" } ], "input": [ { "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_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_2548", "term": "Sequence feature table format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://protein.bio.unipd.it/download/", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "http://protein.bio.unipd.it/mobidblite/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btx015", "pmid": "28453683", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MobiDB-lite: Fast and highly specific consensus prediction of intrinsic disorder in proteins", "abstract": "Motivation: Intrinsic disorder (ID) is established as an important feature of protein sequences. Its use in proteome annotation is however hampered by the availability of many methods with similar performance at the single residue level, which have mostly not been optimized to predict long ID regions of size comparable to domains. Results: Here, we have focused on providing a single consensus-based prediction, MobiDB-lite, optimized for highly specific (i.e. few false positive) predictions of long disorder. The method uses eight different predictors to derive a consensus which is then filtered for spurious short predictions. Consensus prediction is shown to outperform the single methods when annotating long ID regions. MobiDB-lite can be useful in large-scale annotation scenarios and has indeed already been integrated in the MobiDB, DisProt and InterPro databases.", "date": "2017-05-01T00:00:00Z", "citationCount": 139, "authors": [ { "name": "Necci M." }, { "name": "Piovesan D." }, { "name": "Dosztanyi Z." }, { "name": "Tosatto S.C.E." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "University of Padua, Department of Biomedical Sciences, BioComputing UP lab", "email": null, "url": "http://protein.bio.unipd.it/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "ELIXIR-ITA-PADOVA", "email": null, "url": "http://elixir.bio.unipd.it/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Silvio C.E. Tosatto", "email": "silvio.tosatto@unipd.it", "url": "http://protein.bio.unipd.it", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-PADOVA", "additionDate": "2018-03-12T09:45:00Z", "lastUpdate": "2024-11-25T14:39:51.264257Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }