Life Science Protein File AuditOffline, 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. Does not predict protein structures, assess folding accuracy, or validate molecular geometry.https://github.com/lostlight530/life-science-ecosystem-lab/tree/main/bio_toollife-science-protein-file-auditbiotools:life-science-protein-file-audit0.4.0Command-line toolhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0080Sequence analysisWindowsLinuxMacPythonMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_2955Sequence report

Computes counts and source digests; flags uncertain codes without inferring function or sequence correctness.ls-bio protein-fasta --input protein.fasta --output fasta-report.jsonhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_2955Sequence report

Counts only observed C-alpha residues in the first PDB model; not a geometry or fold quality assessment.ls-bio protein-pdb --input structure.pdb --output pdb-report.jsonhttps://github.com/lostlight530/life-science-ecosystem-labRepositorySource repository; the tool is in the bio_tool directoryhttps://workflowhub.eu/workflows/2347Otherrelated knowledge workflow in the same lab.https://github.com/lostlight530/life-science-ecosystem-lab/issuesIssue trackerBug reports and feature requests for ls-bio via GitHub Issueshttps://github.com/lostlight530/life-science-ecosystem-lab/archive/refs/heads/main.zipSource codeLatest source code from the main branch; contents change over time. For the archived 0.4.0 release, use Zenodo DOI 10.5281/zenodo.23447089mainhttps://github.com/lostlight530/life-science-ecosystem-lab/blob/main/bio_tool/README.mdUser manualInstallation, ls-bio protein-fasta and protein-pdb commands, supported inputs, bounded JSON outputs, 8 MB input limit, CWL wrappers and stated limitations10.5281/zenodo.23447088OtherSoftware archive (Zenodo concept DOI) for citing the tool; not a peer-reviewed articleXuanyi Jianglostlight520@gmail.comhttps://github.com/lostlight530/life-science-ecosystem-labhttps://orcid.org/0009-0001-3617-0832PersonPrimary contactDeveloperMaintainerProviderSupportDocumentorContributorDesigned 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 documentationpeptide-mass (Peptide.Express)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. Packaged from the Peptide.Express open peptide-reference-data repository. For laboratory research use only. Not for human or veterinary use.https://github.com/Peptide-Express/peptide-reference-datapeptideexpress-peptide-massbiotools:peptideexpress-peptide-mass0.1.1LibraryCommand-line toolPythonMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0398Protein molecular weight calculationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_1519Peptide molecular weightshttp://edamontology.org/format_2330Textual format

Computes monoisotopic and average peptide masses and ESI [M+nH]n+ m/z values from amino-acid sequences.https://peptide.express/OtherPublisher: Peptide.Expresshttps://doi.org/10.5281/zenodo.23284819OtherZenodo dataset DOIhttps://pypi.org/project/peptide-mass/Downloads pagePyPI packagehttps://github.com/Peptide-Express/peptide-reference-data#readmeGeneralPeptide.Expressinfo@peptide.expresshttps://peptide.express/InstituteDeveloperProviderToolyard BioFree collection of 67 DNA and protein sequence tools and 44 lab calculators that run in the web browser, including reverse complement, translation, ORF finder, restriction maps, pairwise alignment, primer Tm, CRISPR guide finder, codon optimization, plasmid maps, and molarity, dilution, qPCR ΔΔCt and IC50 calculators. Sequences are processed on the user's device and never uploaded.https://webtoolyard.com/seq/toolyard_biobiotools:toolyard_bioWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3912Genetic engineeringWindowsMacLinuxFreewareMatureFree of chargeOpen accesshttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0863Sequence alignment

http://edamontology.org/operation_0431Restriction site recognitionhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/operation_0308PCR primer designhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/operation_0286Codon usage analysishttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/operation_0233Sequence conversionhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank format

http://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/operation_0236Sequence composition calculationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTATaproot Solutions LLChttps://webtoolyard.com/support/Peptide Calculator ProFree browser-based calculators for peptide sequences and solutions. From a one-letter amino acid sequence it computes average molecular weight, monoisotopic mass, molecular formula and m/z for charge states, with N-terminal acetylation, C-terminal amidation and disulfide options. It also computes net charge at a chosen pH, isoelectric point (pI) and GRAVY using EMBOSS pKa values. A concentration calculator converts peptide mass and volume to mg/mL, mM or µM from the molecular weight. All calculations run client-side and no login is required.https://peptidecalculatorpro.org/peptide_calculator_probiotools:peptide_calculator_proWeb applicationhttp://edamontology.org/topic_0123Protein propertieshttp://edamontology.org/topic_3292Biochemistryhttp://edamontology.org/topic_3314ChemistryLinuxWindowsMacJavaScriptProprietaryFree of chargeOpen accesshttp://edamontology.org/operation_0398Protein molecular weight calculationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1964plain text format (unformatted)

http://edamontology.org/data_1519Peptide molecular weights

http://edamontology.org/operation_0403Protein isoelectric point calculationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1964plain text format (unformatted)

http://edamontology.org/data_1528Protein isoelectric point

http://edamontology.org/data_0845Molecular charge

http://edamontology.org/operation_3434Conversion

http://edamontology.org/data_2140Concentration

https://peptidecalculatorpro.org/peptide-molecular-weight-calculator/OtherPeptide molecular weight calculatorhttps://peptidecalculatorpro.org/peptide-net-charge-calculator/OtherPeptide net charge and isoelectric point calculatorhttps://peptidecalculatorpro.org/peptide-concentration-calculator/OtherPeptide concentration calculatorDiffLogoDiffLogo is an easy-to-use tool to visualize motif differences.https://bioconductor.org/packages/DiffLogodifflogobiotools:difflogo2.36.0Command-line toolLibraryhttp://edamontology.org/topic_0622GenomicsMacWindowsLinuxRGPL-2.0-or-laterBioConductorhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_3033Matrix formathttp://edamontology.org/format_1919Sequence record formathttp://edamontology.org/data_2082Matrixhttp://edamontology.org/format_3033Matrix formathttp://edamontology.org/format_1919Sequence record formathttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_3033Matrix formathttp://edamontology.org/format_1919Sequence record formathttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_3033Matrix formathttp://edamontology.org/format_1919Sequence record format

http://edamontology.org/data_2884Plothttp://edamontology.org/format_3508PDFhttp://edamontology.org/format_3603PNG

https://github.com/mgledi/DiffLogo/Mirrorhttps://github.com/mgledi/DiffLogo/Source codehttps://bioconductor.org/packages/DiffLogoUser manual"Grau""Keilwagen""Lando""Nettling""Treutler"cpersonpersonpersonpersonpersonpersonrole = crole = crole = crole = crole = cBRAINPackage for calculating aggregated isotopic distributions and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). This is an implementation of the BRAIN algorithm.https://bioconductor.org/packages/BRAINbrainbiotools:brain1.58.0RRID:SCR_003018rridCommand-line toolLibraryhttp://edamontology.org/topic_3370Analytical chemistryhttp://edamontology.org/topic_0153Lipidomicshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_2269Statistics and probabilityMacWindowsLinuxRGPL-2.0BioConductorProteomicshttp://edamontology.org/operation_3632Isotopic distributions calculationhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_3441Plottinghttp://edamontology.org/data_1857Atomic occupancyhttp://edamontology.org/format_3554R file formathttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_3554R file format

http://edamontology.org/data_2884Plothttp://edamontology.org/format_3579JPGhttp://edamontology.org/format_3603PNG

https://bioconductor.org/packages/release/bioc/src/contrib/BRAIN_1.58.0.tar.gzSource codehttps://bioconductor.org/packages/BRAINUser manualbiostringsuses10.1021/ac303439mPrimaryPiotr Dittwaldwith contributions of Dirk Valkenborg and Jurgen ClaesenRcpiA molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.https://bioconductor.org/packages/Rcpircpibiotools:rcpi1.48.0LibraryCommand-line toolhttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/topic_0078ProteinsMacWindowsLinuxRArtistic-2.0BioConductorhttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_1196SMILEShttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_1196SMILES

http://edamontology.org/data_2884Plothttp://edamontology.org/format_3033Matrix formathttp://edamontology.org/format_3547Image format

http://edamontology.org/data_2854Position-specific scoring matrixhttp://edamontology.org/format_3033Matrix formathttp://edamontology.org/format_3547Image format

http://nanx.me/Rcpi/Mirrorhttps://github.com/road2stat/RcpiMirrorhttps://github.com/nanxstats/RcpiSource codehttps://nanx.me/Rcpi/Source codehttps://bioconductor.org/packages/RcpiUser manual10.1093/bioinformatics/btu624Dong-Sheng CaoPersonDeveloperNan XiaoPersonDeveloperMaintainerQing-Song XuPersonDevelopermsaThe 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.https://bioconductor.org/packages/msamsabiotools:msa1.44.1LibraryCommand-line toolhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_3168SequencingMacLinuxWindowsJavaScriptGPL-2.0-or-laterRostlab toolsBioconductorBioJSBioConductorMatureFree of chargehttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1984FASTA-aln

http://edamontology.org/data_1270Feature tablehttp://edamontology.org/format_2305GFF

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1984FASTA-aln

http://edamontology.org/data_1711Sequence alignment imagehttp://edamontology.org/format_3547Image format

http://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1929FASTA

Visualizes multiple sequence alignment, calculates conservation, shows sequence logo, applies multiple color schemes A multiple sequence alignment (ClustalW, FASTA, ...) Exports selected sequences and regions from the alignment Images are exported in PNG Export sequences in FASTA format Export features in GFF NOTE: Actually, all these output types of data should instead be under separate "constant" operations, while the visualisation should be an unary operation, perhaps without an output.http://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1935GCGhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1935GCGhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1948nbrf/pir

http://edamontology.org/data_0867Sequence alignment reporthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3508PDF

http://github.com/wilzbach/msaHelpdeskhttp://www.bioinf.jku.at/software/msa/Mirrorhttps://github.com/wilzbach/msaRepositoryhttp://biojs.io/Software cataloguehttps://github.com/UBod/msaSource codehttps://bioconductor.org/packages/msaUser manual10.1093/bioinformatics/btv494Christoph KainrathPersonDeveloperEnrico BonatestaPersonDeveloperUlrich BodenhoferPersonDeveloperMaintainerProteinIQBrowser-based bioinformatics platform for running protein structure prediction, molecular docking, protein design, molecular dynamics, sequence analysis, and related life-science workflows without local installation.https://proteiniq.io/proteiniqbiotools:proteiniqWeb applicationWeb APIBioinformatics portalWorkbenchhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/topic_0077Nucleic acidsProprietaryMatureFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_0474Protein structure predictionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_1477mmCIF

Representative function. Exact inputs, outputs, formats, and settings depend on the selected ProteinIQ tool.http://edamontology.org/operation_0478Molecular dockinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_1477mmCIFhttp://edamontology.org/data_2301SMILES stringhttp://edamontology.org/format_1196SMILES

http://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_1477mmCIF

Representative docking function. ProteinIQ supports multiple docking methods with tool-specific ligand formats, preparation options, scores, poses, and downloadable structures.http://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_2048Report

Representative sequence-analysis function. Available reports and computed properties vary by the selected tool.http://edamontology.org/operation_4008Protein designhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_1477mmCIF

http://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_1477mmCIF

Representative design function. Individual ProteinIQ tools may design sequences, structures, binders, peptides, antibodies, or other molecular candidates.https://proteiniq.io/app/toolsServiceBrowse the available ProteinIQ tools.https://proteiniq.io/contactHelpdeskhttps://www.linkedin.com/company/proteiniq/Social mediahttps://x.com/ProteinIQSocial mediahttps://www.reddit.com/r/ProteinIQ/Discussion forumhttps://proteiniq.io/api/v1/openapi.jsonAPI specificationOpenAPI specification for the ProteinIQ public API.https://proteiniq.io/docsGeneralhttps://proteiniq.io/docs/start-guideQuick start guidehttps://proteiniq.io/docs/apiAPI documentationhttps://proteiniq.io/docs/api/python-sdkAPI documentationhttps://proteiniq.io/legal/termsTerms of use10.3390/ijms26189189UsagePublication reporting use of ProteinIQ for peptide-property calculations.Matic Brozsupport@proteiniq.iohttps://proteiniq.io/authors/matic-brozhttps://orcid.org/0009-0008-4134-4631PersonDeveloperMaintainerProviderDocumentorSupportPrimary contactFounder and developer of the ProteinIQ platform and hosted service. Individual scientific tools retain their original authorship and licensing.ProteinIQhttps://proteiniq.io/ProjectProviderMaintainerSupportCognitionBioChemA structural pharmacology workbench for cognition-related CNS targets, built so that a displayed number must trace to a computation. Runs Boltz-2 locally for structure prediction, validates chemistry with RDKit, enforces a provenance record on every value, and reports eight studies pre-registered under content hashes before any data was seen. Its headline result is negative: designed peptides did not separate from composition-matched shuffles of their own amino acids.https://github.com/hopejsh/CognitionBioChemcognitionbiochembiotools:cognitionbiochem1.0.0doi:10.5281/zenodo.22032684doiconcept DOI, resolves to the latest releasedoi:10.5281/zenodo.22032685doi1.0.0RRID:SCR_028851rridWeb applicationCommand-line toolhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_3336Drug discoveryMacLinuxPythonJavaScriptApache-2.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0474Protein structure predictionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1477mmCIF

Boltz-2 v2.2.1 runs locally; every predicted structure is retained under content-addressed custody with its confidence files.http://edamontology.org/operation_2428Validationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1477mmCIF

http://edamontology.org/data_1460Protein structure

Backbone geometry, per-residue pLDDT and interface PAE are read from the model's own file; a value that was never computed renders as a label.http://edamontology.org/operation_2480Structure analysishttp://edamontology.org/data_2301SMILES stringhttp://edamontology.org/format_1196SMILES

http://edamontology.org/data_1463Small molecule structure

RDKit validation: parsing, molecular formula, InChIKey and stereochemistry completeness. A SMILES that fails to parse is shown as unverified.https://github.com/hopejsh/CognitionBioChemRepositoryhttps://github.com/hopejsh/CognitionBioChem/issuesIssue trackerhttps://github.com/hopejsh/CognitionBioChem/archive/refs/tags/v1.0.0.tar.gzSource code1.0.0https://github.com/hopejsh/CognitionBioChem#readmeGeneralhttps://github.com/hopejsh/CognitionBioChem/blob/main/docs/REGISTRATION.mdCitation instructionshttps://github.com/hopejsh/CognitionBioChem/blob/main/NOTICETerms of useThe `license` field above is Apache-2.0, which covers this project's code, but the repository is not single-licensed. It redistributes third-party scientific data that keeps its own terms: CC BY 4.0 (UniProt, AlphaFold DB), CC BY-SA 3.0 (ChEMBL-derived files -- SHARE-ALIKE, so reuse carries an obligation onward), CC0 1.0 (RCSB depositions) and MIT (Boltz-2 model outputs). NOTICE lists which files fall under which.Seung Ho Jungseung.jung@gmail.comhttps://orcid.org/0000-0001-7914-5306PersonDeveloperMaintainerpeptide-qcpeptide-qc analyzes a standard peptide sequence and returns residue composition, elemental formula, average and monoisotopic mass, approximate charge and pI, and Kyte-Doolittle hydropathy. It is a deterministic command-line tool and JavaScript library for research software tests and teaching. It does not identify unknown samples, certify purity, model unusual chemistry or provide clinical interpretation.https://peptidomexico.com.mx/calculadora/peptide-qcbiotools:peptide-qc0.1.0Command-line toolLibraryhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0080Sequence analysisWindowsMacLinuxJavaScriptMIThttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_2087Molecular property

Outputs deterministic sequence composition and approximate physicochemical properties for standard residues.npx peptide-qc analyze --sequence ACDEFGHIK --ph 7 --jsonhttps://github.com/PeptidoMexico/peptidomexico-open-scienceRepositoryhttps://github.com/PeptidoMexico/peptidomexico-open-science/issuesIssue trackerhttps://www.npmjs.com/package/peptide-qcSoftware package0.1.0https://github.com/PeptidoMexico/peptidomexico-open-scienceSource code0.1.0https://peptidomexico-open-science.readthedocs.io/en/latest/peptide-qc/User manualQuick start guidehttps://github.com/PeptidoMexico/peptidomexico-open-science/blob/main/CITATION.cffCitation instructionsPéptido Méxicohola@peptidomexico.com.mxhttps://peptidomexico.com.mx/DeveloperMaintainerProviderProSeqGOProSeqGO predicts Gene Ontology (GO) terms for protein sequences using ESM2 embeddings and a trained 1-Dimensional Convolutional Neural Network multi-label classifier. By integrating recent advances in protein language models, ProSeqGO facilitates large-scale, automated functional annotation directly from sequence input, empowering researchers to infer protein function, explore biological mechanisms, and accelerate discovery in genomics and proteomics.https://proseqgo.com/proseqgobiotools:proseqgov1.0.0Web serviceCommand-line toolBashSQLPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_1777Protein function predictionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_2858Ontology concept

Predicts the probability of Gene Ontology (GO) term membership for an input protein sequence using ESM2 embeddings and 1D CNNhttps://github.com/BehRoooz/proseqgoRepositoryhttps://github.com/BehRoooz/proseqgo/releasesSource codeRFdiffusionRFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc).https://github.com/RosettaCommons/RFdiffusionRFdiffusionbiotools:RFdiffusionv1.1.0Command-line toolhttp://edamontology.org/topic_0082Structure predictionPythonShellOtherMaturehttp://edamontology.org/operation_0476Ab initio structure predictionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

https://sites.google.com/omsf.io/rfdiffusion/overviewGeneral10.1038/s41586-023-06415-837433327PMC10468394SPALNGenome mapping and spliced alignment of cDNA or amino acid sequenceshttps://github.com/ogotoh/spalnspalnbiotools:spalnver.3.0.8bCommand-line toolhttp://edamontology.org/topic_0102MappingCPerlC++GPL-2.0Maturehttp://edamontology.org/operation_2429Mappinghttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/data_1234Sequence set (nucleic acid)

http://edamontology.org/data_0863Sequence alignment

https://github.com/ogotoh/spalnRepositoryhttps://github.com/ogotoh/spalnGeneral10.1093/nar/gkag35742134803PMC1317563310.1093/bioinformatics/btn4601872804310.1093/nar/gks70822848105PMC348821110.1093/bioinformatics/16.3.1901086901210.1093/bioinformatics/btae51739152995PMC1136180910.1007/978-1-0716-1036-7_53328988710.1093/bioinformatics/btl06716500940Osamu Gotohgotoh.osamu.67a@st.kyoto-u.ac.jphttps://orcid.org/0009-0002-6750-1945Personshicshic is a collection of shims for use in automated workflow compositionhttps://github.com/magnuspalmblad/shicshicbiotools:shicScriptMITFree of chargeOpen accessProteomicsGalaxyMetabolomicshttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_3747protXML

http://edamontology.org/data_2872ID listhttp://edamontology.org/format_3475TSV

http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3651MGF

http://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3651MGF

http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0870Sequence distance matrixhttp://edamontology.org/format_1912Nexus format

http://edamontology.org/data_0870Sequence distance matrixhttp://edamontology.org/format_1991mega

http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/format_3475TSV

http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3655pepXML

http://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_3475TSV

http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3247mzIdentML

http://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_3475TSV

http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0972Text mining reporthttp://edamontology.org/format_2332XML

http://edamontology.org/data_1174ChEBI IDhttp://edamontology.org/format_3475TSV

http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3475TSV

http://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3247mzIdentML

http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_3475TSV

http://edamontology.org/data_2872ID listhttp://edamontology.org/format_3475TSV

http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3655pepXML

http://edamontology.org/data_1009Protein namehttp://edamontology.org/format_2330Textual format

http://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3655pepXML

http://edamontology.org/data_2764Protein name (UniProt)http://edamontology.org/format_2330Textual format

https://github.com/magnuspalmblad/shicRepositoryhttps://github.com/magnuspalmblad/shic/blob/main/README.mdGeneralMagnus Palmbladmagnus.palmblad@gmail.comhttps://orcid.org/0000-0002-5865-8994Primary contactVeit Schwämmlehttps://orcid.org/0000-0002-9708-6722Dirk Winkelhardthttps://orcid.org/0000-0001-8770-2221Vedran Kasalicahttps://orcid.org/0000-0002-0097-1056Anna-Lena Lamprechthttps://orcid.org/0000-0003-1953-5606GPCRchimeraDBGPCRchimeraDB: A database to support the design of novel chimeric G-Protein Coupled Receptors (GPCRs) to unravel signaling pathways, characterize key regions and facilitate the design of new receptors for drug discovery. It is the first database to centralize chimeric GPCRs into one central repository, offering extensive descriptions at the sequence, structural, and biophysical levels through user-friendly visualization tools, while linking them to their parent GPCRs. Furthermore, GPCRchimeraDB expands the description of natural GPCRs compared to existing databases like GPCRdb and IUPHAR by including their biophysical profiles and integrating an interactive sequence-structure (1D-3D) visualization tool which helps to keep an overview of the large amount of data. Finally, GPCRchimeraDB incorporates a sequence alignment tool that has been demonstrated to outperform the current state-of-the-art tool for non-conventional GPCRs, which are critical targets in drug discovery.https://bio2byte.be/gpcrchimeradbgpcrchimeradbbiotools:gpcrchimeradb2025-12.v1Database portalhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_3292Biochemistryhttp://edamontology.org/topic_3398BioengineeringCC-BY-4.03D-BioInfo-Protein-Ligand-InteractionsgpcrOpen access3D-BioInfoBelgiumhttp://edamontology.org/operation_3431Data depositionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/data_1017Sequence rangehttp://edamontology.org/data_2872ID listhttp://edamontology.org/data_0897Protein propertyhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/data_0970Citation

http://edamontology.org/data_2019Map data

http://edamontology.org/data_2884Plot

http://edamontology.org/data_0897Protein property

http://edamontology.org/data_1277Protein features

http://edamontology.org/data_1233Sequence set (protein)

10.1016/j.jmb.2025.16916440268234PrimaryPathoFact2An Integrative Pipeline for Antimicrobial Resistance Genes, Virulence Factors, Toxin-associated proteins, and Biosynthetic Gene Clusters Prediction in Metagenomeshttps://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2pathofact2biotools:pathofact22.0Command-line toolhttp://edamontology.org/topic_4013Antimicrobial resistanceLinuxPythonRBashGPL-3.0Free of chargeOpen accesshttp://edamontology.org/operation_3482Antimicrobial resistance predictionhttp://edamontology.org/operation_3461Virulence predictionhttp://edamontology.org/data_0925Sequence assemblyhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_2048Report

https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2Repositoryhttps://zenodo.org/records/14192463Repositoryhttps://zenodo.org/records/17647372RepositoryLuis F. Delgadoluis.delgado@uni.luhttps://orcid.org/0000-0001-7850-5285Júlia Ortís Sunyerjulia.ortissunyer@uni.luhttps://orcid.org/0000-0002-2714-7067Paul Wilmespaul.wilmes@uni.luhttps://orcid.org/0000-0002-6478-2924prolfquappA command-line tool for differential expression analysis in quantitative proteomicshttps://github.com/prolfqua/prolfquappprolfquappbiotools:prolfquapp0.1.6Command-line toolhttp://edamontology.org/topic_0121ProteomicsMacLinuxRMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3741Differential protein expression profilinghttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3620xlsxhttp://edamontology.org/format_2331HTML

./prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANN # and again you run the version within the docker container with # ./prolfquapp_docker.sh prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANNhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3620xlsx

http://edamontology.org/data_3914Quality control reporthttp://edamontology.org/format_2331HTML

http://edamontology.org/operation_0571Expression data visualisationhttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_2603Expression datahttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_3508PDF

https://github.com/prolfqua/prolfquappRepositoryhttps://github.com/prolfqua/prolfquapp/issuesIssue trackerhttps://github.com/prolfqua/prolfquapp/releases/tag/0.1.6Downloads page0.1.6https://github.com/prolfqua/prolfquapp/blob/master/README.mdGeneral10.1021/acs.jproteome.4c00911Primary0.0.6PeptideShakerPeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics datahttp://compomics.github.io/projects/peptide-shaker.htmlpeptideshakerbiotools:peptideshaker3.0.11Desktop applicationCommand-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0644ProteomeMacLinuxJavaApache-2.0de.NBIProteomicsBioInfra.ProtOpen accesshttp://edamontology.org/operation_3694Mass spectrum visualisationhttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_3755PTM localisationhttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3651MGF

http://edamontology.org/data_2992Protein structure imagehttp://edamontology.org/format_3579JPGhttp://edamontology.org/format_3604SVG

http://edamontology.org/data_3754GO-term enrichment datahttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2969Sequence imagehttp://edamontology.org/format_3547Image format

http://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_3475TSV

https://github.com/compomics/peptide-shakerSource codehttp://compomics.github.io/projects/peptide-shaker.html#read-meGeneral10.1038/nbt.310925574629PrimaryBioInfra.ProtInstituteProviderDominik Kopczynskdominik.kopczynski@isas.dehttp://compomics.github.io/projects/peptide-shaker.htmlPersonPrimary contactNGPSimulation of next-generation proteomics (NGP) based on single-molecule sequencing.https://github.com/magnuspalmblad/NGPngpbiotools:ngphttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_3869Simulationhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3508PDF

10.1021/acs.jproteome.1c0013633904308PMC8185883PrimaryEPIKPrecise and scalable evolutionary placement with informative k-mers.https://github.com/phylo42/EPIKepikbiotools:epik0.2.0Command-line toolhttp://edamontology.org/topic_0084PhylogenyLinuxMacC++PythonMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0323Phylogenetic inferencehttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0955Data indexhttp://edamontology.org/format_2333Binary format

http://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_3464JSON

10.1093/BIOINFORMATICS/BTAD69237975872PMC107010970.2.0Nikolai Romashchenkonromashchenko@lirmm.frhttps://orcid.org/0000-0002-2264-5219PersonEric Rivalsrivals@lirmm.frhttps://orcid.org/0000-0003-3791-3973PersonDDGembPredicting the impact of mutations on protein stability from sequence using protein language modelshttps://ddgemb.biocomp.unibo.itddgembbiotools:ddgemb1http://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3325Rare diseasesMatureFree of chargeOpen accessToolsRare Diseases3D-BioInfoItalyhttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/data_3498Sequence variations

http://edamontology.org/data_0896Protein report

https://ddgemb.biocomp.unibo.it/help/General10.1093/bioinformatics/btaf01939799516PMC11783275PrimaryELIXIR-ITA-BOLOGNAhttps://www.biocomp.unibo.itInstituteProviderCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonMaintainerDeveloperPrimary contactUniversalMerUniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists.https://ugrammer.github.ioUniversalMerbiotools:UniversalMer2.0.0Command-line toolhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_0080Sequence analysisWindowsMacC++CFreewareEmergingFree of chargeOpen accessToolsUKhttp://edamontology.org/operation_3472k-mer countinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2546FASTA-likehttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_2546FASTA-likehttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2546FASTA-like

http://edamontology.org/data_1266Base word frequencies table

http://edamontology.org/data_1265Base frequencies table

http://edamontology.org/data_3671Text

https://sourceforge.net/projects/universal-mer/Mirrorhttps://sourceforge.net/projects/universal-mer/Command-line specification2.0ProteinPromptA webserver for predicting protein-protein interactions.http://proteinformatics.org/ProteinPromptproteinpromptbiotools:proteinpromptWeb applicationhttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_3957Protein interaction experimenthttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0154Small moleculesMacLinuxWindowsPythonFree of chargeOpen accesshttp://edamontology.org/operation_2492Protein interaction predictionhttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_2464Protein-protein binding site predictionhttp://edamontology.org/data_2976Protein sequencehttps://gitlab.hzdr.de/proteinprompt/ProteinPromptRepository10.1101/2021.09.03.458859René Staritzbichlerrene.staritzbichler@medizin.uni-leipzig.dehttps://orcid.org/0000-0002-6719-2997Peter W. Hildebrandhttps://orcid.org/0000-0003-0063-1104Sebastian Canzlerhttps://orcid.org/0000-0001-7935-9582Markus FischerDavid UlbrichtNikola RisticPEP-FOLD4PEP-FOLD4 is a fast and accurate structure prediction tool for peptides of up to 40 amino acids in aqueous solutions. Unlike many machine-learning approaches (e.g., AlphaFold2, TrRosetta, RaptorX), it integrates the Debye-Hückel formalism for charged side-chain interactions with a Mie potential for intramolecular forces. Based on a coarse-grained representation, PEP-FOLD4 performs competitively on well-structured peptides and shows significant improvements for poly-charged peptides, making it particularly useful for studying pH- and salt-dependent conformations.https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4pep-fold4biotools:pep-fold4Web applicationhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_3332Computational chemistryPythonMatureFree of chargeOpen access3D-BioInfoFrancehttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/operation_0476Ab initio structure predictionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_2884Plothttp://edamontology.org/format_1475PDB database entry format

http://edamontology.org/data_2048Report

https://mobyle2.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-FOLD4ServiceLink to the PEP-FOLD4 web page servicehttps://owncloud.rpbs.univ-paris-diderot.fr/owncloud/index.php/s/7NHDSJXiQA0V2zySource codeSource code and recipe for docker images allowing to run PEP-FOLD4 locally. All repository content is covered by a non-commercial license agreement and may be used for non-commercial and internal research purposes only.https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4/User manual10.1093/nar/gkad37637166962PMC10320157PrimaryJulien Reyjulien.rey@u-paris.frhttps://orcid.org/0000-0002-3050-511XPersonSupportDeveloperPrimary contactSamuel Murailsamuel.muriail@u-paris.frhttps://orcid.org/0000-0002-3842-5333PersonContributorSjoerd de Vrieshttps://orcid.org/0000-0002-7701-3454PersonContributorPhilippe Derreumauxphilippe.derreumaux@ibpc.frPersonContributorPierre Tufférypierre.tuffery@inserm.frhttps://orcid.org/0000-0003-1033-9895PersonContributorProteoMakerProteoMaker is a platform for the generation of an in-silico bottom-up proteomics data set with a ground truth on the level of proteoforms.https://github.com/computproteomics/ProteoMakerproteomakerbiotools:proteomakerLibraryWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3524Simulation experimentMacLinuxWindowsRMITProteomicsMatureFree of chargeOpen accesshttp://edamontology.org/operation_3566Simulated gene expression data generationhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_3112Gene expression matrixhttp://edamontology.org/format_3752CSV

http://edamontology.org/data_1238Proteolytic digesthttp://edamontology.org/format_3752CSV

http://edamontology.org/data_3914Quality control reporthttp://edamontology.org/format_3750YAML

http://edamontology.org/data_0951Statistical estimate scorehttp://edamontology.org/format_3752CSV

https://computproteomics.bmb.sdu.dk/app_direct/ProteoMakerServiceWeb applicationhttps://github.com/computproteomics/ProteoMakerSource codePHIEmbedPHIEmbed is a phage-host interaction prediction tool that uses protein language models to represent the receptor-binding proteins of phages. It presents improvements over using handcrafted (manually feature-engineered) sequence properties and eliminates the need to manually extract and select features from phage sequences.https://github.com/bioinfodlsu/phage-host-predictionphiembedbiotools:phiembedCommand-line toolhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0781VirologyMacLinuxWindowsPythonMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_3752CSV

Predicts the host genus of a phage given its receptor-binding protein sequenceshttps://github.com/bioinfodlsu/phage-host-predictionRepositoryhttp://phiembed.bioinfodlsu.com/Servicehttps://github.com/bioinfodlsu/phage-host-predictionSource codehttps://github.com/bioinfodlsu/phage-host-predictionInstallation instructionsQuick start guideCitation instructionsCommand-line options10.1371/journal.pone.028903037486915PrimaryMark Edward M. Gonzalesgonzales.markedward@gmail.comhttps://github.com/memgonzaleshttps://orcid.org/0000-0001-5050-3157PersonDeveloperResearch Assistant, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, PhilippinesJennifer C. Uretajennifer.ureta@gmail.comhttps://scholar.google.com/citations?user=v0Tf_u4AAAAJ&hl=enhttps://orcid.org/0000-0003-0427-5311PersonContributorFaculty, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, PhilippinesAnish M.S. Shresthaanish.shrestha@dlsu.edu.phhttps://a-transposable-element.com/https://orcid.org/0000-0002-9192-9709PersonPrimary contactHead, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, PhilippinesSVMHCPrediction of MHC class I binding peptides.http://www.sbc.su.se/%7Epierre/svmhc/svmhcbiotools:svmhc1Web applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_1277Protein features

10.1186/1471-2105-3-2512225620PMC129981Primarybils.seInstituteProviderarne@bioinfo.sePersonPrimary contactMDR databaseMedium-chain dehydrogenases/reductases database.http://www.bioinfo.ifm.liu.se/services/mdr/mdrbiotools:mdrDatabase portalhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_1277Protein features

10.1110/ps.035428.10818614751PMC2548362Primarybils.seInstituteProvideryohell@ifm.liu.sePersonPrimary contactDRIP-PREDDisorder/order prediction for proteins.http://www.sbc.su.se/%7Emaccallr/disorder/cgi-bin/submit.cgidrip-predbiotools:drip-pred1Web applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_1277Protein features

10.1007/s10858-009-9386-z19915800PMC2797623Otherbils.seInstituteProvidermaccallr@sbc.su.sePersonPrimary contactTreeFamSearch of TreeFam's HMM collection, allows query sequence to be aligned (MAFFT) and inserted into tree (RAxML) to significantly matching models.http://www.treefam.org/searchtreefambiotools:treefam1Web applicationhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0623Gene and protein familiesLinuxWindowsMacEBI Toolshttp://edamontology.org/operation_0323Phylogenetic tree generationhttp://edamontology.org/operation_0239Sequence motif recognitionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_0858Sequence signature matches

https://treefam.tenderapp.com/Helpdeskhttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.treefam.org/helpGeneral10.1093/nar/gkj11816381935PMC1347480OtherFabian SchreiberPersonDeveloperMateus PatricioPersonDeveloperEMBL-EBIInstituteProviderhttps://treefam.tenderapp.com/PersonPrimary contactFabian Schreiberfs@ebi.ac.ukPersonPrimary contactLigSearchIdentifies small molecules likely to bind to given protein.http://www.ebi.ac.uk/thornton-srv/databases/LigSearchligsearchbiotools:ligsearch1Web applicationhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0128Protein interactionsLinuxWindowsMacThornton ToolsEBI Toolshttp://edamontology.org/operation_2575Protein binding site predictionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_1566Protein-ligand interaction report

http://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.ebi.ac.uk/thornton-srv/databases/LigSearchGeneral10.1107/s090744491302229424311580PMC3852652Roman LaskowskiPersonDeveloperTjaart de BeerPersonDeveloperThornton GroupPersonDeveloperEMBL-EBIInstituteProvidertjaart@ebi.ac.ukPersonPrimary contactRoman Laskowskiroman@ebi.ac.ukPersonPrimary contactSASAnnotation of protein sequence with structural info from similar proteins in the PDB.http://www.ebi.ac.uk/thornton-srv/databases/sassasbiotools:sas1Web applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxWindowsMacThornton ToolsEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_1476PDB

The ouput is an alignment of the query sequence vs a sequence from PDB, annotated by structural datahttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.ebi.ac.uk/thornton-srv/databases/sasGeneral10.1093/protein/11.10.8559862203PrimaryRoman LaskowskiPersonDeveloperThornton GroupPersonDeveloperDuncan MilburnContributorEMBL-EBIInstituteProviderroman@ebi.ac.ukPersonPrimary contactRoman Laskowskiroman@ebi.ac.ukPersonPrimary contactTabhuWeb server for antibody humanisation specifically designed to help researcher in each step of a humanisation experiment. It provides tools to: Select the suitable humane template; Select the grafting region; Predict the non-human and humanised antibody paratope; Select the minimum set of back-mutations to retain the parental binding affinity; Build the three-dimensional humanised antibody model and check its structure.http://www.biocomputing.it/tabhutabhubiotools:tabhu1.0Web applicationhttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMachttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_1460Protein structure

Tool for AntiBody Humanizationhttp://circe.med.uniroma1.it/tabhu/help.phpGeneral10.1093/bioinformatics/btt36923803466PMC3753563PrimaryELIXIR-ITA-SAPIENZAInstituteProviderPier Paolo Olimpieripierpaolo.olimpieri@gmail.comPersonPrimary contactDIGITA database of immunoglobulin variable domain sequences and related search and modelling tools.http://www.biocomputing.it/digit/digitbiotools:digitDatabase portalhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0082Structure predictionLinuxWindowsMachttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/operation_0361Sequence annotationhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_0896Protein report

A database of immunoglobulin variable domain sequences and related search and modelling toolshttp://circe.med.uniroma1.it/digit/about.phpGeneral10.1093/nar/gkr80622080506PMC3245095PrimaryELIXIR-ITA-SAPIENZAInstituteProviderPaolo Marcatilipaolo.marcatili@gmail.comPersonPrimary contactSWIPETool for performing rapid local alignment searches in amino acid or nucleotide sequence databases. It is a highly optimized implementation of the Smith-Waterman algoritm using SIMD parallel computing technology available on common CPUs.http://dna.uio.no/swipeswipebiotools:swipe2.0.5Command-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3047Molecular biologyLinuxC++AGPL-3.0MatureFree of chargehttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/data_2977Nucleic acid sequence

http://edamontology.org/data_1383Sequence alignment (nucleic acid)

http://edamontology.org/data_1384Sequence alignment (protein)

https://github.com/torognes/swipeRepositoryhttps://github.com/torognes/swipeSource codehttp://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-221Citation instructionshttp://dna.uio.no/swipe/General10.1186/1471-2105-12-22121631914PMC3120707PrimaryTorbjørn RognesPersonDeveloperUiOInstituteProvidertorognes@ifi.uio.noPersonPrimary contactJAliAlignment method for comparing a protein sequence to a protein family, represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is a generalization of the Smith-Waterman algorithm.http://bibiserv.cebitec.uni-bielefeld.de/jalijalibiotools:jali1.3Web APIWeb applicationCommand-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacCBiGide.NBIMatureFree of chargehttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3154Protein alignmenthttp://edamontology.org/format_1929FASTAComputes Jumping ALIgnments from a protein sequence and an alignment of a protein family.http://bibiserv.cebitec.uni-bielefeld.de/jali?id=jali_view_downloadRepositoryhttp://bibiserv.cebitec.uni-bielefeld.de/jali?id=jali_view_downloadSource codehttp://bibiserv.cebitec.uni-bielefeld.de/resources/download/jaliBinarieshttp://bibiserv.cebitec.uni-bielefeld.de/jali?id=jali_view_manualGeneral10.1089/10665270276103417212487762PrimaryJens StoyePersonDeveloperCeBiTecInstituteProviderBielefeld UniversityInstituteProviderBiBiServInstituteProviderbibi-help@cebitec.uni-bielefeld.dePersonPrimary contactTOPCONSConsensus prediction of membrane protein topology.http://topcons.cbr.su.se/topconsbiotools:topcons1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacJavahttp://edamontology.org/operation_0270Transmembrane protein analysishttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_1277Protein features

http://topcons.cbr.su.se/pred/help/General10.1093/nar/gkv48525969446PMC4489233Primarybils.seInstituteProviderarne@bioinfo.sePersonPrimary contactSCAMPIPrediction of membrane protein topology from first principles.http://scampi.cbr.su.se/scampibiotools:scampi1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_0270Transmembrane protein analysishttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_1277Protein features

http://scampi.cbr.su.se/pred/help/General10.1093/bioinformatics/btv70926644416Primarybils.seInstituteProviderarne@bioinfo.sePersonPrimary contactOnD-CRFPredicting order and disorder in proteins using conditional random fields.http://babel.ucmp.umu.se/ond-crf/ond-crfbiotools:ond-crf1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_1277Protein features

http://babel.ucmp.umu.se/ond-crf/about.phpGeneral10.1093/bioinformatics/btn261PMC3139103Primarybils.seInstituteProvideruwe@ucmp.umu.sePersonPrimary contactOCTOPUSPrediction of membrane protein topology and signal peptides.http://octopus.cbr.su.se/octopusbiotools:octopus1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_0270Transmembrane protein analysishttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_1277Protein features

http://octopus.cbr.su.se/index.php?about=helpGeneral10.1093/bioinformatics/btn22118474507Primarybils.seInstituteProviderarne@bioinfo.sePersonPrimary contactFragHMMentResidue-residue contact prediction.http://predictioncenter.org/Services/FragHMMent/descr.htmlfraghmmentbiotools:fraghmment1Web applicationhttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMacJavahttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_1277Protein features

http://predictioncenter.org/Services/FragHMMent/descr.htmlGeneral10.1093/bioinformatics/btp14919289446PMC2677742Primarybils.seInstituteProvidertorgeir.hvidsten@umu.sePersonPrimary contactFISH - sequence searchFamily Identification with Structure Anchored Hidden Markov Models.http://babel.ucmp.umu.se/fish/hmmpfam.htmfish_sequence_searchbiotools:fish_sequence_search1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_1277Protein features

http://babel.ucmp.umu.se/fish/about.phpGeneral10.1093/nar/gkl33016844969PMC1538871Primarybils.seInstituteProvideruwe@ucmp.umu.sePersonPrimary contactAMYPdbAn online database dedicated to amyloid precursor families and to their amino acid sequence signatures.http://amypdb.genouest.orgamypdbbiotools:amypdbDatabase portalhttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMacPHPJavaScriptSQLMatureFree of chargehttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1093Sequence accessionhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2200FASTA-like (text)

http://edamontology.org/data_1233Sequence set (protein)http://edamontology.org/format_1332FASTA search results format

http://amypdb.genouest.org/e107_plugins/amypdb_project/help.phpGeneral10.1186/1471-2105-9-27318544157PMC2442844Primaryolivier.collin@irisa.frPersonPrimary contactchristian.delamarche@univ-rennes1.frPersonPrimary contactPICRProtein Identifier Cross Reference service to map proteins by identifiers and sequence.http://www.ebi.ac.uk/Tools/picr/picrbiotools:picr1Web applicationhttp://edamontology.org/topic_3345Data identity and mappinghttp://edamontology.org/topic_3071Data managementLinuxWindowsMacEBI Toolshttp://edamontology.org/operation_3282ID mappinghttp://edamontology.org/data_2907Protein accessionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_2907Protein accession

http://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.ebi.ac.uk/Tools/picr/init.do#documentationGeneralhttp://www.ebi.ac.uk/Tools/picr/RESTDocumentation.doAPI documentationMap accession numbers between databases. It will also retrieve the UPI(UniProt Archive (UniParc) identifier of the given accession number.10.1186/1471-2105-8-40117945017PMC2151082PrimaryRichard Cotercote@ebi.ac.ukPersonDeveloperEMBL-EBIhttp://www.ebi.ac.uk/InstituteProviderPRIDE supportpride-support@ebi.ac.ukPersonPrimary contacthttp://www.ebi.ac.uk/support/PersonPrimary contactUniProt AlignMultiple sequence alignment.http://www.uniprot.org/alignuniprot_alignbiotools:uniprot_align1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacCC-BY-ND-3.0UniProt ToolsEBI Toolshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_0863Sequence alignment

http://www.uniprot.org/contactHelpdeskhttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.uniprot.org/help/sequence-alignmentsGeneralhttp://www.uniprot.org/help/licenseTerms of use10.1093/nar/gku98925348405PMC4384041PrimaryUniProt Consortiumhttp://www.uniprot.org/help/aboutInstituteProviderEMBL-EBIhttp://www.ebi.ac.uk/InstituteProviderhttp://www.uniprot.org/contactPersonPrimary contactXavier Watkinswatkins@ebi.ac.ukPersonPrimary contactMODORAMAAt MODORAMA two applications can be run: MODexplorer, an integrated tool for exploring protein sequence, structure and function relationships, and MODalign, a rich alignment editor to improve target-template alignmentshttp://modorama.orgmodoramabiotools:modorama1.0Web applicationhttp://edamontology.org/topic_0082Structure predictionLinuxWindowsMachttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_2089Sequence alignment refinementhttp://edamontology.org/operation_0474Protein structure predictionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_0893Sequence-structure alignmentMODexplorer: Explores sequence, structure and function relationships in protein families and selects templates and perform homology modeling; MODalign: displays, evaluates and edits alignments for comparative (homology) modelinghttp://modorama.org/General10.1093/bioinformatics/btt06223396123PMC3605600Primary10.1093/bioinformatics/bts07022308148PMC3315710OtherELIXIR-ITA-SAPIENZAInstituteProviderJan Kosinskisupport@modorama.orgPersonPrimary contactGPCRHMMA hidden Markov model for GPCR detection.http://gpcrhmm.sbc.su.se/gpcrhmmbiotools:gpcrhmm1Command-line toolWeb applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_1277Protein features

http://gpcrhmm.sbc.su.se/instructions.htmlGeneral10.1110/ps.05174590616452613PMC2249772Primarybils.seInstituteProviderhttp://www.sbc.su.se/~erison/PersonPrimary contactHSYMDOCKSymmetric protein docking for oligomers with Cn or Dn symmetry from the structure or sequence of a subunit molecule.http://huanglab.phys.hust.edu.cn/hsymdock/hsymdockbiotools:hsymdock2018-06-02Web applicationhttp://edamontology.org/topic_2275Molecular modellingLinuxWindowsMacPHPhttp://edamontology.org/operation_0478Molecular dockinghttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/format_1476PDBhttp://huanglab.phys.hust.edu.cn/hsymdock/help.htmlGeneral10.1093/nar/gky39829846641PMC6030965Primaryhuanglab@hust.edu.cnPersonPrimary contactMobiDB-liteMobiDB-lite is an optimized method for highly specific predictions of long intrinsically disordered regionshttp://protein.bio.unipd.it/mobidblite/mobidb-litebiotools:mobidb-lite1.0Command-line toolhttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxPythonCC-BY-NC-ND-4.0Maturehttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_2480Structure analysishttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_2548Sequence feature table format

http://protein.bio.unipd.it/download/Software packagehttp://protein.bio.unipd.it/mobidblite/General10.1093/bioinformatics/btx01528453683University of Padua, Department of Biomedical Sciences, BioComputing UP labhttp://protein.bio.unipd.it/ELIXIR-ITA-PADOVAhttp://elixir.bio.unipd.it/Silvio C.E. Tosattosilvio.tosatto@unipd.ithttp://protein.bio.unipd.itPersonPrimary contact