shicshic 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 contactmsaDisplay multiple-sequence alignment. The tool is also available as 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.http://msa.biojs.netmsabiotools:msa1.0.0Command-line toolLibraryhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_3168SequencingLinuxWindowsMacJavaScriptApache-2.0Rostlab toolsBioconductorBioJSMatureFree 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_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

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

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_1948nbrf/pirhttp://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/data_2976Protein sequencehttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1935GCGhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank format

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

https://github.com/wilzbach/msaRepositoryhttp://biojs.io/Software cataloguehttp://github.com/wilzbach/msaHelpdeskhttp://www.bioinf.jku.at/software/msa/Mirrorhttps://github.com/wilzbach/msaSource codehttps://cdn.bio.sh/Binarieshttps://github.com/wilzbach/msa/blob/master/LICENSETerms of usehttp://msa.biojs.netGeneral10.1093/bioinformatics/btw47427412096PMC5181560Primary10.1093/bioinformatics/btv49426315911OtherSebastian WilzbachPersonDeveloperIan SillitoeContributorGuy YachdavContributorBenedikt RauscherContributorTatyana GoldbergContributorTechnische Universität MünchenInstituteProviderGoogle Summer of Code (GSoC) 2014Funding agencyContributorBioJSInstituteProviderhttp://github.com/wilzbach/msaPersonPrimary contactUlrich Bodenhoferbodenhofer@bioinf.jku.atPersonPrimary 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 contactRosettaESAn automated tool that uses a fragment-based sampling strategy for de novo model completion of macromolecular structures from cryo-EM density maps at 3–5-Å resolution.https://www.rosettacommons.org/rosettaesbiotools:rosettaesPlug-inhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_0611Electron microscopyhttp://edamontology.org/topic_1317Structural biologyLinuxWindowsMacOtherMatureFree of charge (with restrictions)http://edamontology.org/operation_3443Image analysishttp://edamontology.org/operation_2480Structure analysishttp://edamontology.org/data_1710Structure imagehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0889Structural profilehttp://edamontology.org/format_2032Workflow format

https://www.rosettacommons.org/docs/latest/release-notesAPI specificationhttps://media.nature.com/original/nature-assets/nmeth/journal/v14/n8/extref/nmeth.4340-S2.pdfGeneral10.1038/nmeth.434028628127PMC6009829Frank Dimaiodimaio@u.washington.eduPersonPrimary contactUNRES serverA server implementation of the UNRES package for coarse-grained simulations of protein structures with the physics-based UNRES model. It can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be runhttp://unres-server.chem.ug.edu.pl/unresbiotools:unresWeb applicationhttp://edamontology.org/topic_0176Molecular dynamicshttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_0593NMRhttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_0476Ab initio structure predictionhttp://edamontology.org/data_1127PDB IDhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_1537Protein structure report

http://unres-server.chem.ug.edu.pl/tutorialTraining material10.1093/nar/gky32829718313PMC6031057Cezary Czaplewskicezary.czaplewski@ug.edu.plPersonPrimary contactAdam Liwoadam.liwo@ug.edu.plPersonPrimary contactproABCPredictor of Antibody-Antigen interactions based on the Random Forest Algorithm. User submitted sequences are automatically aligned and annotated according to their source organism and germline families.http://www.biocomputing.it/proABCproabcbiotools:proabc1.0Web applicationhttp://edamontology.org/topic_0081Structure analysisLinuxWindowsMachttp://edamontology.org/operation_2492Protein interaction predictionhttp://edamontology.org/operation_0474Protein structure predictionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_0906Protein interaction data

proABC estimates the residue-based probability for three different kind of interactions: Non-bonded Interactions, Hydrogen Bonds and Hydrophobic Interactions.http://circe.med.uniroma1.it/proABC/help_proABC.phpGeneral10.1093/bioinformatics/btt36923803466PMC3753563PrimaryELIXIR-ITA-SAPIENZAInstituteProviderPier Paolo Olimpieripierpaolo.olimpieri@gmail.comPersonPrimary contactSTITCHResource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.http://stitch.embl.de/stitchbiotools:stitchCommand-line toolWeb applicationDatabase portalhttp://edamontology.org/topic_3314Chemistryhttp://edamontology.org/topic_3344Biomedical sciencehttp://edamontology.org/topic_0602Molecular interactions, pathways and networksLinuxWindowsMachttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_3083Pathway or network visualisationhttp://edamontology.org/operation_2497Pathway or network analysishttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2299Gene namehttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_1199InChIKeyhttp://edamontology.org/format_1196SMILEShttp://edamontology.org/format_3468xlshttp://edamontology.org/data_1009Protein namehttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_0990Compound namehttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2546FASTA-like

http://edamontology.org/data_2600Pathway or networkhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_3547Image format

http://edamontology.org/data_0954Database cross-mappinghttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2042Evidencehttp://edamontology.org/format_2330Textual format

STITCH is a database of protein – chemical interactions that integrates many sources of experimental and manually curated evidence with text-mining information and interaction predictions. Its key function is to provide users with predictions about the interactions that their entities of interest (proteins or small molecules) may be making with other such entities, and to visualise where a set of entities of interest can be found within the STITCH network. Direct traceable links to the original sources on which interactions are described in the network, make it easy for users to trace the provenance of the data.http://stitch.embl.de/cgi/show_info_page.pl?UserId=pRfi11Qlkhnx&sessionId=sEfmbh_T7QLqGeneral10.1093/nar/gkm79518084021PMC2238848Primary10.1093/nar/gkp93719897548PMC2808890Other10.1093/nar/gkt120724293645PMC3964996Other10.1093/nar/gkr101122075997PMC3245073OtherEMBLhttp://www.embl.org/Funding agencyContributorSUND-KUhttp://healthsciences.ku.dk/Funding agencyContributorEC FP6http://ec.europa.eu/research/index.cfmFunding agencyContributorBMBFhttps://www.bmbf.de/Funding agencyContributorEMBOhttp://www.embo.org/Funding agencyContributorCPRhttp://www.cpr.ku.dk/Funding agencyContributorTUDhttp://www.biotec.tu-dresden.de/Funding agencyContributorHD-HuBhttps://www.hd-hub.de/InstituteProviderMichael Kuhnhttp://stitch1.embl.de/cgi/show_info_page.plDeveloperMichael Kuhnhttp://stitch1.embl.de/cgi/show_info_page.plPersonPrimary contactSODAProtein SOlubility based on Disorder and Aggregationhttp://protein.bio.unipd.it/soda/soda-solubilitybiotools:soda-solubility1.0Web APIWeb applicationhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_3538Protein disordered structurehttp://edamontology.org/topic_2814Protein structure analysisLinuxWindowsMacPythonCC-BY-NC-ND-4.0Maturehttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_3475TSV

http://protein.bio.unipd.it/soda/helpGeneral10.1093/nar/gkx41228505312PMC7059794PrimaryUniversity 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.ithttp://orcid.org/0000-0003-4525-7793PersonPrimary contactRAVEN ToolboxThe RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.https://github.com/SysBioChalmers/RAVENraven_toolboxbiotools:raven_toolbox2.0Command-line toolScripthttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_2259Systems biologyhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_3398BioengineeringLinuxWindowsMacMATLABGPL-3.0MatureFree of chargehttp://edamontology.org/operation_3439Pathway or network predictionhttp://edamontology.org/operation_3660Metabolic network modellinghttp://edamontology.org/operation_2497Pathway or network analysishttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1208proteinhttp://edamontology.org/data_2600Pathway or networkhttp://edamontology.org/format_2585SBMLhttp://edamontology.org/format_3620xlsxhttp://edamontology.org/data_3112Gene expression matrixhttp://edamontology.org/format_3752CSV

http://edamontology.org/data_2600Pathway or networkhttp://edamontology.org/format_2585SBMLhttp://edamontology.org/format_3620xlsxhttp://edamontology.org/format_3750YAML

http://edamontology.org/data_3722Physiology parameterhttp://edamontology.org/format_1957raw

https://gitter.im/SysBioChalmers/RAVENMailing listGitter chat roomhttps://github.com/SysBioChalmers/RAVEN/issuesIssue trackerGitHub Issueshttps://github.com/SysBioChalmers/RAVENRepositoryGitHub Repositoryhttps://github.com/SysBioChalmers/RAVEN/wikiHelpdeskGitHub Wikihttps://github.com/SysBioChalmers/RAVEN/releasesBinariesStabile releaseshttps://github.com/SysBioChalmers/RAVENSource codeSource codehttps://github.com/SysBioChalmers/RAVEN/wikiGeneralGitHub Wiki10.1101/321067Primaryhttps://gitter.im/SysBioChalmers/RAVEN?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badgePersonPrimary contactHao Wanghao.wang@chalmers.sehttp://orcid.org/0000-0001-7475-0136PersonPrimary contactPIGSWeb server for the automatic modeling of immunoglobulin variable domains based on the canonical structure method. It has a user-friendly and flexible interface, that allows the user to choose templates (for the frameworks and the loops) and modeling strategies in an automatic or manual fashion.http://circe.med.uniroma1.it/pigs/pigsbiotools:pigs1Web applicationhttp://edamontology.org/topic_0082Structure predictionLinuxWindowsMachttp://edamontology.org/operation_0474Protein structure predictionhttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_1460Protein structure

Automatic prediction of immunoglobulin structures.http://circe.med.uniroma1.it/pigs/help.phpGeneral10.1038/nprot.2014.18925375991Other10.1093/bioinformatics/btn34118641403OtherELIXIR-ITA-SAPIENZAInstituteProviderPaolo Marcatilipaolo.marcatili@gmail.comPersonPrimary contactSIB-BLASTSIB-BLAST is a web server for improved delineation of true and false positives in PSI-BLAST searches using the SimpleIsBeautiful (SIB) algorithm for sequence based homology detection.http://bioserv.mps.ohio-state.edu/sib-blast/sib-blastbiotools:sib-blastWeb applicationhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_3315MathematicsLinuxWindowsMacBLAST utilityhttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2976Protein sequence

http://edamontology.org/data_0857Sequence search results

http://bioserv.mps.ohio-state.edu/sib-blast/Manual.htmlUser manual10.1093/nar/gkp30119429693PMC2703926Ralf Bundschuhbundschuh@mps.ohio-state.eduPersonPrimary contactAUTOHDAnalysis of H/D-exchange data using isotopic distributions.http://www.ms-utils.org/autohd.htmlautohdbiotools:autohdCommand-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacCGPL-3.0ms-utilsProteomicshttp://edamontology.org/operation_0404Protein hydrogen exchange rate calculationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2200FASTA-like (text)

http://edamontology.org/data_1537Protein structure reporthttp://edamontology.org/format_2330Textual format

http://ms-utils.orgSoftware cataloguehttp://www.ms-utils.org/autohd_download.htmlSource codehttp://www.ms-utils.org/autohd_download.htmlSource codehttp://www.ms-utils.org/autohd.htmlGeneral10.1016/s1044-0305(01)00301-411720389Magnus Palmbladmagnus.palmblad@gmail.comPersonMaintainerwebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentorBioLCCCAn analytic model of peptide retention.http://theorchromo.ru/biolcccbiotools:biolcccWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacms-utilsProteomicshttp://edamontology.org/operation_3633Retention time predictionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2979Peptide propertyhttp://edamontology.org/format_2331HTML

http://ms-utils.orgSoftware cataloguehttp://packages.python.org/pyteomics.biolccc/API/mespaceBioLCCC.htmlSource codehttp://theorchromo.ru/General10.1021/ac060913x17105170webmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentordecoy.plDecoy database generator from Matrix Science.http://www.matrixscience.com/help/decoy_help.htmldecoy.plbiotools:decoy.plCommand-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxMacPerlms-utilsProteomicshttp://edamontology.org/operation_0364Random sequence generationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2546FASTA-like

http://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2546FASTA-like

http://ms-utils.orgSoftware cataloguehttp://www.matrixscience.com/downloads/decoy.pl.gzSource codehttp://www.matrixscience.com/downloads/decoy.pl.gzSource codehttp://www.matrixscience.com/help/decoy_help.html#MANUALGeneral10.1038/nmeth78516118637Primarywebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentormassXpertTool for analysis of polymer and peptide/protein mass spectra.http://www.massxpert.orgmassxpertbiotools:massxpertmassXpert 2Desktop applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3292Biochemistryhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3511Nucleic acid sites, features and motifshttp://edamontology.org/topic_0123Protein propertieshttp://edamontology.org/topic_0601Protein modificationsms-utilsProteomicshttp://edamontology.org/operation_0365Nucleic acid restriction digesthttp://edamontology.org/operation_0417Post-translation modification site predictionhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_2929Protein fragment weight comparisonhttp://edamontology.org/operation_0239Sequence motif recognitionhttp://edamontology.org/operation_3023Prediction and recognition (protein)http://edamontology.org/operation_3024Prediction and recognition (nucleic acid)http://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/data_0977Tool identifierhttp://edamontology.org/format_2332XMLhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2332XML

http://edamontology.org/data_0977Tool identifierhttp://edamontology.org/format_2332XML

http://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2332XML

http://ms-utils.orgSoftware cataloguehttp://download.tuxfamily.org/massxpert/source/Source code10.1093/bioinformatics/btp50419740912PrimarymassXpertmassxpert-maintainer@massxpert.orgPersonMaintainerwebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentorProtterInteractive protein feature visualization and integration with experimental proteomic data.http://wlab.ethz.ch/protter/protterbiotools:protterWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_3542Protein secondary structurehttp://edamontology.org/topic_3534Protein binding sitesLinuxWindowsMacJavams-utilsProteomicshttp://edamontology.org/operation_2241Transmembrane protein visualisationhttp://edamontology.org/operation_2486Topology diagram drawinghttp://edamontology.org/operation_0472GPCR predictionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_3636MRM/SRMhttp://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_3747protXMLhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_2547uniprotkb-like formathttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/format_3747protXMLhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_2547uniprotkb-like formathttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_3747protXMLhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_2547uniprotkb-like formathttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1709Protein secondary structure imagehttp://edamontology.org/format_3603PNGhttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_3508PDF

http://ms-utils.orgSoftware cataloguehttp://ulo.github.io/Protter/Source codehttp://wlab.ethz.ch/protter/help/General10.1093/bioinformatics/btt60724162465Ulrich Omasitsprotter@imsb.biol.ethz.chPersonMaintainerwebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentor