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{ "count": 33278, "next": "?page=2", "previous": null, "list": [ { "name": "BOLD-Local-DB", "description": "BOLD-Local-DB converts the public TSV/tar.gz data package downloaded from BOLD Systems into a local, indexed SQLite database that can be searched entirely offline. It has two components: a Creator (desktop GUI) that filters, imports, indexes, and optionally adds full-text search to the downloaded data; and a local web viewer for advanced field search, full-text search, batch search by term list, and CSV/FASTA export. Intended for researchers who need to query large BOLD exports (DNA barcode records, taxonomy, collection metadata) repeatedly without depending on an internet connection or BOLD's rate limits.", "homepage": "https://github.com/etovarluque/BOLD-Local-DB", "biotoolsID": "bold-local-db", "biotoolsCURIE": "biotools:bold-local-db", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3489", "term": "Database management" }, { "uri": "http://edamontology.org/topic_3050", "term": "Biodiversity" }, { "uri": "http://edamontology.org/topic_0077", "term": "Nucleic acids" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "PolyForm-Noncommercial-1.0.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/etovarluque/BOLD-Local-DB/tree/main/guide", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [], "owner": "etovar", "additionDate": "2026-08-25T14:46:59.814690Z", "lastUpdate": "2026-08-25T15:10:18.822564Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Folklore", "description": "Deterministic, rule-based variant interpretation platform for clinical genetics laboratories. Automates ACMG/AMP 2015 classification using a Bayesian point-based framework (Tavtigian et al. 2018) with BayesDel ClinGen SVI-calibrated thresholds (Pejaver et al. 2022). Integrates 8 reference databases (gnomAD v4.1, ClinVar, dbNSFP 4.9c, SpliceAI, gnomAD Constraint, HPO, ClinGen, Ensembl VEP). Analyzes nuclear and mtDNA variants, structural and copy-number variants (SV/CNV), with trio/family and cohort analysis. Supports HPO-based phenotype matching, biomedical literature mining across 2M+ PubMed publications, and structured clinical report generation. AI assists in evidence synthesis but does not make classification decisions. EU-hosted on dedicated infrastructure in Helsinki, Finland (GDPR-compliant).", "homepage": "https://folklore.helena.bio", "biotoolsID": "HelixInsight", "biotoolsCURIE": "biotools:HelixInsight", "version": [ "3.39.1" ], "otherID": [ { "value": "RRID:SCR_028669", "type": "rrid", "version": "3.39.1" } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0920", "term": "Genotype/phenotype report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1622", "term": "Disease report" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0305", "term": "Literature search" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "Proprietary", "collectionID": [], "maturity": "Mature", "cost": "Commercial", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/helena-bioinformatics/folklore-mcp", "type": [ "Repository" ], "note": "Public Apache-2.0 MCP protocol adapter source; the Folklore SaaS platform and clinical interpretation backend remain proprietary." }, { "url": "https://api.helena.bio/folklore/v1/mcp", "type": [ "Service" ], "note": "Public remote endpoint for Folklore Clinical Variant Interpretation MCP version 1.2.2." }, { "url": "https://registry.modelcontextprotocol.io/v0.1/servers?search=io.github.helena-bioinformatics%2Ffolklore&version=latest", "type": [ "Software catalogue" ], "note": "Official MCP Registry entry: io.github.helena-bioinformatics/folklore." }, { "url": "https://folklore.helena.bio/integrations", "type": [ "Other" ], "note": "Official Folklore integrations and MCP client connection page." }, { "url": "https://api.helena.bio/folklore/v1/health", "type": [ "Technical monitoring" ], "note": "Public health and discovery metadata endpoint for the Folklore MCP service." } ], "download": [ { "url": "https://github.com/helena-bioinformatics/folklore-mcp", "type": "Source code", "note": "Apache-2.0 standalone MCP protocol adapter. Excludes proprietary clinical interpretation logic, private data, credentials and operational infrastructure.", "version": "1.2.2" } ], "documentation": [ { "url": "https://folklore.helena.bio/docs", "type": [ "General" ], "note": "Complete production documentation covering every threshold, database version, and classification rule. Intended for clinical geneticists, laboratory directors, accreditation auditors, and bioinformaticians." }, { "url": "https://folklore.helena.bio/how-it-works", "type": [ "General" ], "note": "Seven-stage analysis pipeline (quality control, annotation, classification, phenotype matching, literature, screening, interpretation) transforming a raw VCF into a clinician-ready report, each stage producing traceable, auditable output." }, { "url": "https://folklore.helena.bio/methodology", "type": [ "General" ], "note": "ACMG/AMP 2015 classification methodology (Richards et al. 2015) via Bayesian point-based system (Tavtigian et al. 2018), BayesDel ClinGen SVI-calibrated thresholds (Pejaver et al. 2022), and SpliceAI aligned to ClinGen SVI 2023 (Walker et al. 2023). Optional ClinGen VCEP overlay for ~50-60 genes. Strictly evidence-based, no ML determines pathogenicity." }, { "url": "https://folklore.helena.bio/methodology/mtdna", "type": [ "General" ], "note": "Mitochondrial DNA variant classification under the ClinGen Mitochondrial Disease Working Group (MMDWG) 2020 specification (McCormick et al. 2020). Operates as an independent module from the nuclear ACMG/AMP pipeline; every variant carries an explicit framework provenance label. Strength tiers follow ClinGen mtDNA VCEP v1.0.0." }, { "url": "https://folklore.helena.bio/methodology/family-analysis", "type": [ "General" ], "note": "Inheritance-aware evidence from trio (proband + both parents), duo, and proband-plus-sibling analyses. Implements ClinGen SVI 2018 de novo PS2/PM6 (PMID 29543229), Jarvik & Browning 2016 LOD segregation framework (PMID 27236918), and ClinGen SVI 2021 PP1 strength bands. Augments the existing ACMG/AMP classification without re-calling variants." }, { "url": "https://folklore.helena.bio/methodology/sv", "type": [ "General" ], "note": "Structural and copy-number variant evaluation under the Riggs 2020 joint ACMG/ClinGen technical standard. Documents the point-based loss and gain metrics, dosage-sensitivity evidence, and five-tier classification, with reference data and documented limitations." }, { "url": "https://folklore.helena.bio/screening-methodology", "type": [ "General" ], "note": "Prioritizes classified variants for clinical review. After ACMG classification determines what each variant is, screening determines which to review first based on patient-specific clinical relevance. Evaluates seven independent dimensions, applies clinical profile boosts, and produces a four-tier priority ranking with transparent, visible score components." }, { "url": "https://folklore.helena.bio/docs/folklore-connector", "type": [ "API documentation" ], "note": "Canonical connector guide for Folklore Clinical Variant Interpretation MCP (io.github.helena-bioinformatics/folklore), version 1.2.2." }, { "url": "https://github.com/helena-bioinformatics/folklore-mcp#readme", "type": [ "General" ], "note": "Public Apache-2.0 MCP protocol adapter README. The Folklore SaaS platform and clinical interpretation backend remain proprietary." }, { "url": "https://github.com/helena-bioinformatics/folklore-mcp/blob/main/CHANGELOG.md", "type": [ "Release notes" ], "note": "Release history for the public Folklore MCP protocol adapter." } ], "publication": [ { "doi": "10.5281/zenodo.21105027", "pmid": null, "pmcid": null, "type": [ "Preprint" ], "version": "1.0", "note": "Methodological framework for real-world performance studies of the platform's variant classification, demonstrated on three internal validation cohorts.", "metadata": null }, { "doi": "10.5281/zenodo.21189571", "pmid": null, "pmcid": null, "type": [ "Preprint" ], "version": "1.0", "note": "A Deterministic Classification Core with an Agentic Interpretation Layer: An Architecture for Auditable, Human-Gated Clinical Variant Analysis", "metadata": null }, { "doi": "10.5281/zenodo.21763096", "pmid": null, "pmcid": null, "type": [ "Preprint" ], "version": null, "note": "Robustness and cross-cohort concordance of developmental regulons in endometrial carcinoma. Authors: Draga Toncheva, Vasil Sgurev and Vladimir Mitev.", "metadata": null }, { "doi": "10.5281/zenodo.21922952", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": "1.2.2", "note": "Archived public Apache-2.0 Folklore MCP adapter release. All-version DOI: 10.5281/zenodo.21922951.", "metadata": null }, { "doi": "10.5281/zenodo.22093164", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": "1.3.1", "note": "Archived public Apache-2.0 Folklore MCP adapter release with four read-only tools, including semantic Literature Corpus search. All-version DOI: 10.5281/zenodo.21922951.", "metadata": null } ], "credit": [ { "name": "Helena Bioinformatics", "email": "contact@helena.bio", "url": "https://helena.bio", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Developer" ], "note": null } ], "owner": "helenabio", "additionDate": "2026-02-23T13:56:07.187145Z", "lastUpdate": "2026-08-25T12:53:12.573956Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "snoBoard", "description": "The snoBoard database compiles ribosomal RNA (rRNA) modifications, box C/D and box H/ACA snoRNA guides sequences for a number of species including Saccharomyces cerevisiae (Sc), Human (Hs), the plant Arabidopsis thaliana (At) and tomato Solanum lycopersicum (Sl). Mapped modifications are 2’-O methylation, pseudouridylation and other known modifications when available. The user interface allows the access to rRNA targets, mapped modifications and snoRNA guides under different views. Modifications can be accessed through a table (one line per modification), or mapped on their target RNA sequences and secondary structures. A comparative view allows to access to mapped sites conserved between a selected subset of species. Using the comparative view, it is possible to interrogate and visualize the conservation of target nucleotides sequences and modified sites. Information on modifications targets and snoRNA guides can be accessed by organism, snoRNA guide family and modification type.", "homepage": "https://snoboard.org/", "biotoolsID": "snoboard", "biotoolsCURIE": "biotools:snoboard", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_3295", "term": "Epigenetics" } ], "operatingSystem": [], "language": [], "license": "GPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Julien Touchais", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Philippe Bordron", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-1975-0920", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact" ], "note": null }, { "name": "Christine Gaspin", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0304-5186", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Primary contact" ], "note": null }, { "name": "GenoToul bioinformatics facility", "email": null, "url": "https://bioinfo.genotoul.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "pbordron", "additionDate": "2026-08-25T12:23:12.640164Z", "lastUpdate": "2026-08-25T12:23:22.038683Z", "editPermission": { "type": "group", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PanAbyss", "description": "PanAbyss is a tool for exploring and visualizing pangenome graphs. It allows users to search for and display regions of a pangenome using coordinates on a reference individual or based on annotations. It also enables searching for regions associated with a selected set of individuals (for example, those linked to a phenotype), computing proximity trees, and retrieving sequences from a given region.", "homepage": "https://github.com/Pange31/PanAbyss", "biotoolsID": "panabyss", "biotoolsCURIE": "biotools:panabyss", "version": [ "1.4.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [], "license": "GPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/Pange31/PanAbyss", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/Pange31/PanAbyss/wiki", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Graziani", "email": "fabien.graziani@inrae.fr", "url": null, "orcidid": "https://orcid.org/0009-0002-3966-0906", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "GenoToul bioinformatics facility", "email": null, "url": "https://bioinfo.genotoul.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "fabien", "additionDate": "2026-06-29T09:42:44.084698Z", "lastUpdate": "2026-08-25T11:50:05.748155Z", "editPermission": { "type": "group", "authors": [ "pbordron" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Pan1c", "description": "Pan1c is a Snakemake workflow that simplifies the creation of pangenomes by focusing on the comparison of similar chromosomes, using either PGGB or Minigraph-Cactus.\nA pangenome graph is first generated individually for each chromosome, and then these chromosome-scale pangenomes are concatenated into a final graph. This approach reduces construction time through parallelization and facilitates interpretation as well as downstream analyses. Throughout the process, various graphs and statistics are produced to help users assess the quality of the pangenome graph and interpret the results.\nAll these visualizations and statistics are accessible via a web page generated by Pan1c-view.", "homepage": "https://forge.inrae.fr/genotoul-bioinfo/Pan1c/pan1c", "biotoolsID": "pan1c", "biotoolsCURIE": "biotools:pan1c", "version": [ "1.14" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3796", "term": "Population genomics" }, { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" } ], "operatingSystem": [ "Linux" ], "language": [], "license": "AGPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://forge.inrae.fr/genotoul-bioinfo/Pan1c/pan1c", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://forge.inrae.fr/genotoul-bioinfo/Pan1c/pan1c/-/wikis/home", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.64898/2026.04.17.719212", "pmid": null, "pmcid": null, "type": [ "Preprint" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Alexis Mergez", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Martin Racoupeau", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Philippe Bardou", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-0004-0251", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Christophe Klopp", "email": "christophe.klopp@inrae.fr", "url": null, "orcidid": "https://orcid.org/0000-0001-7126-5477", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "GenoToul bioinformatics facility", "email": null, "url": "https://bioinfo.genotoul.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "pbordron", "additionDate": "2026-08-25T10:04:25.598750Z", "lastUpdate": "2026-08-25T11:40:00.095755Z", "editPermission": { "type": "group", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CubexSoft OLM to PST Converter for Mac", "description": "CubexSoft OLM to PST Converter for Mac & Windows is a powerful and user-friendly tool designed to convert OLM files into PST format quickly and securely. It allows Mac users to migrate emails, contacts, calendars, tasks, notes, and other mailbox data while maintaining the original folder structure and data integrity. The software supports batch conversion, preserves email formatting and attachments, and offers a simple interface for hassle-free migration. Users can also download the free demo version to preview and evaluate the conversion process before purchasing the full version.", "homepage": "https://www.cubexsoft.com/olm/pst.html", "biotoolsID": "cubexsoft_olm_to_pst_converter_for_mac", "biotoolsCURIE": "biotools:cubexsoft_olm_to_pst_converter_for_mac", "version": [ "10.0" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "olmtopst", "additionDate": "2026-08-25T10:46:35.666462Z", "lastUpdate": "2026-08-25T10:47:02.190187Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PureJsImage", "description": "PureJsImage is a free, open-source TypeScript library for decoding, inspecting, processing, and converting ordinary images and scientific rasters in Node.js and modern browsers. 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"https://www.phfscience.nz/staff-profiles/rhys-white/", "orcidid": "https://orcid.org/0000-0001-6620-758X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null } ], "owner": "rhys", "additionDate": "2026-08-15T04:20:06.745455Z", "lastUpdate": "2026-08-15T04:20:15.574585Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BRANCHSNV", "description": "BRANCHSNV reports strict clade-exclusive nucleotide markers separately from single-nucleotide substitutions reconstructed on a selected edge of a rooted phylogenetic tree, while retaining ambiguity across equally parsimonious ancestral-state reconstructions.", "homepage": "https://branchsnv.readthedocs.io/en/latest/", "biotoolsID": "branchsnv", "biotoolsCURIE": "biotools:branchsnv", "version": [ "0.1.0" ], "otherID": [ { "value": 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alignment.nex \\\n --tree tree.nwk \\\n --outgroup-file outgroup_tips.txt \\\n --clade-tips clade_tips.txt \\\n --mode both \\\n --output branch_snvs.tsv \\\n --members-output branch_members.txt \\\n --report branchsnv_report.json" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_0194", "term": "Phylogenomics" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/RhysWhite/branchsnv", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/RhysWhite/branchsnv/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/RhysWhite/branchsnv-validation", "type": [ "Other" ], "note": null } ], "download": [ { "url": "https://pypi.org/project/branchsnv/", "type": "Software package", "note": null, "version": null }, { "url": "https://github.com/RhysWhite/branchsnv/releases", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://branchsnv.readthedocs.io/en/latest/", "type": [ "FAQ" ], "note": null }, { "url": "https://branchsnv.readthedocs.io/en/latest/", "type": [ "Citation instructions" ], "note": null } ], "publication": [], "credit": [], "owner": "rhys", "additionDate": "2026-08-14T16:23:03.786354Z", "lastUpdate": "2026-08-14T16:23:14.011790Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "P2Rank", "description": "Novel machine learning-based method for prediction of ligand binding sites from protein structure.", "homepage": "http://siret.ms.mff.cuni.cz/p2rank", "biotoolsID": "p2rank", "biotoolsCURIE": "biotools:p2rank", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2575", "term": "Protein binding site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" }, { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java", "Groovy" ], "license": "MIT", "collectionID": [ "ELIXIR-CZ" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://siret.ms.mff.cuni.cz/p2rank", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s13321-018-0285-8", "pmid": "30109435", "pmcid": "PMC6091426", "type": [], "version": null, "note": null, "metadata": { "title": "P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure", "abstract": "Background: Ligand binding site prediction from protein structure has many applications related to elucidation of protein function and structure based drug discovery. It often represents only one step of many in complex computational drug design efforts. Although many methods have been published to date, only few of them are suitable for use in automated pipelines or for processing large datasets. These use cases require stability and speed, which disqualifies many of the recently introduced tools that are either template based or available only as web servers. Results: We present P2Rank, a stand-alone template-free tool for prediction of ligand binding sites based on machine learning. It is based on prediction of ligandability of local chemical neighbourhoods that are centered on points placed on the solvent accessible surface of a protein. We show that P2Rank outperforms several existing tools, which include two widely used stand-alone tools (Fpocket, SiteHound), a comprehensive consensus based tool (MetaPocket 2.0), and a recent deep learning based method (DeepSite). P2Rank belongs to the fastest available tools (requires under 1 s for prediction on one protein), with additional advantage of multi-threaded implementation. Conclusions: P2Rank is a new open source software package for ligand binding site prediction from protein structure. It is available as a user-friendly stand-alone command line program and a Java library. P2Rank has a lightweight installation and does not depend on other bioinformatics tools or large structural or sequence databases. Thanks to its speed and ability to make fully automated predictions, it is particularly well suited for processing large datasets or as a component of scalable structural bioinformatics pipelines.", "date": "2018-12-01T00:00:00Z", "citationCount": 242, "authors": [ { "name": "Krivak R." }, { "name": "Hoksza D." } ], "journal": "Journal of Cheminformatics" } } ], "credit": [ { "name": "David Hoksza", "email": "hoksza@ksi.mff.cuni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "davidhokszamff", "additionDate": "2018-08-24T13:49:33Z", "lastUpdate": "2026-08-14T09:40:08.820438Z", "editPermission": { "type": "group", "authors": [ "ayan" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ASAP", "description": "ASAP (Assemble Species by Automatic Partitioning) is a method to build species partitions from single locus sequence alignments.\nASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. 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ASAP is efficient enough to split data sets as large 104 sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.", "date": "2021-02-01T00:00:00Z", "citationCount": 15, "authors": [ { "name": "Puillandre N." }, { "name": "Brouillet S." }, { "name": "Achaz G." } ], "journal": "Molecular Ecology Resources" } } ], "credit": [ { "name": "Nicolas Puillandre", "email": "puillandre@mnhn.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Kigaard", "additionDate": "2021-01-18T11:19:37Z", "lastUpdate": "2026-08-14T09:40:06.996761Z", "editPermission": { "type": "group", "authors": [ "arkamukherjee", "keqing", "huda4" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Peptide Reconstitution Calculator", "description": "A transparent, unit-aware calculator for the mathematical relationship between peptide mass, target concentration and solution volume. 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/host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-liver-tumour" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "Run nnUnet pretrained on Task004_Hippocampus MRI data targeting posterior and anterior parts of the hippocampus", "cmd": "docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-hippocampus-segmentation" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": "Run nnUnet pretrained on Task010_Colon targeting are colon cancer primaries.", "cmd": "docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-colon-cancer" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": 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Pharmacophore, which is the spatial arrangement of features that is essential for a molecule to interact with a specific target receptor, is an important model for achieving this goal. We present a freely available web server, named PharmaGist, for pharmacophore detection. The employed method is ligand based. Namely, it does not require the structure of the target receptor. Instead, the input is a set of structures of drug-like molecules that are known to bind to the receptor. The output consists of candidate pharmacophores that are computed by multiple flexible alignment of the input ligands. The method handles the flexibility of the input ligands explicitly and in deterministic manner within the alignment process. PharmaGist is also highly efficient, where a typical run with up to 32 drug-like molecules takes seconds to a few minutes on a stardard PC. Another important characteristic is the capability of detecting pharmacophores shared by different subsets of input molecules. This capability is a key advantage when the ligands belong to different binding modes or when the input contains outliers. 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