PDB-REDO databank of optimised macromolecular structuresDatabank of optimised macromolecular structures. PDB-REDO entries are refined, rebuilt and validated with one consistent protocol using the equivalent entry in the Protein Data Bank and its experimental data. PDB-REDO entries typically have higher structural quality and a better fit to the experimental data.https://pdb-redo.eupdb-redobiotools:pdb-redoDatabase portalhttp://edamontology.org/topic_0081Structure analysisLinuxWindowsMacFreeware3D-BioInfo3D-BioInfo-Nucleic-AcidDRCAT3D-BioInfo-Protein-Ligand-InteractionsINSTRUCT3D-BioInfo-Structure-FunctionMatureFree of chargeOpen accessData3D-BioInfohttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1127PDB ID

http://edamontology.org/data_0883Structurehttp://edamontology.org/format_1477mmCIFhttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1539Protein structural quality reporthttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_3464JSON

http://edamontology.org/data_0937Electron density map

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1454dssp

https://github.com/PDB-REDO/pdb-redo-mainRepositoryRepository for main software pipelinehttps://github.com/PDB-REDO/libpdb-redoRepositoryLibrary code for pdb-redo toolshttps://github.com/PDB-REDO/pdb-redo-session-managerRepositoryRepository for the web interface including the APIhttps://pdb-redo.eu/download-info.htmlDownloads pagehttps://pdb-redo.euGeneral10.1107/s090744491105451522505269PMC332260810.1107/s002188980900878422477769PMC324681910.1107/s090744490803759119171973PMC263163110.1107/s205225251801055230224962PMC612664810.1002/pro.335329168245PMC5818736Method7Algorithms for homology restrains; new databank10.1093/bioinformatics/btr59022034521PMC3232375MethodAlgorithms for model rebuilding10.1016/j.jmb.2016.02.00226869101MethodAlgorithms for correction and completion of N-glycosylation sites10.1107/s205979831601303627710932PMC505313710.1107/s205979831900387530988258PMC6465985Robbie P. Joostenr.joosten@nki.nlhttps://orcid.org/0000-0002-2323-2686PersonPrimary contactDeveloperGert Vriendvriend@cmbi.ru.nlPersonProject initiatorAnastassis Perrakisa.perrakis@nki.nlhttps://orcid.org/0000-0002-1151-6227PersonPrimary contactMaarten Hekkelmanm.hekkelman@nki.nlPersonDeveloperBart van BeusekomPersonContributorKrista JoostenPersonContributorNetherlands Organization for Scientific Research (NWO)Funding agencyVarious grants (Veni, Vidi, TOP)West-Life Horizon 2020ConsortiumiNEXTConsortiumWouter TouwPersonContributorThe Netherlands Cancer InstituteInstituteProviderCCP4https://www.ccp4.ac.ukProjectContributorFinancial and other supportGRNsightWeb application and service for visualizing small- to medium-scale models of gene regulatory networks. It automatically lays out either an unweighted or weighted network graph based on an Excel input spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows. It is best-suited for visualizing networks of fewer than 35 nodes and 70 edges and has general applicability.http://dondi.github.io/GRNsight/grnsightbiotools:grnsight7.8.0Web applicationhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0204Gene regulationLinuxWindowsMacJavaScriptBSD-3-ClauseMatureFree of chargehttp://edamontology.org/operation_1781Gene regulatory network analysishttp://edamontology.org/operation_3083Pathway or network visualisationGRNsight automatically lays out a network graph based on an Excel input spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows. When a user uploads a spreadsheet with an unweighted adjacency matrix, GRNsight automatically lays out the graph using black lines and pointed arrowheads. When a user uploads a spreadsheet with a weighted adjacency matrix, GRNsight uses pointed and blunt arrowheads, and colors the edges and adjusts their thicknesses based on the sign (positive for activation or negative for repression) and magnitude of the weight parameter. Nodes are rectangular and support gene labels of up to 12 characters. The edges are arcs, which become straight lines when the nodes are close together. Self-regulatory edges are indicated by a loop on the lower-right side of a node. Visualizations can be modified by sliders that adjust D3.js's force graph layout parameters and through manual node dragging.https://github.com/dondi/GRNsightRepositoryhttps://github.com/dondi/GRNsight/archive/refs/heads/main.zipSource codehttp://dondi.github.io/GRNsight/documentation.htmlGeneral10.7717/peerj-cs.85Other10.5281/zenodo.7411630OtherAlex MillerPersonDeveloperJia Celyne GarciaPersonDeveloperCindy TongPersonDeveloperAmelie DinhPersonDeveloperMilka ZekariasPersonDeveloperNgoc Kim Ngan TranPersonDeveloperCecilia ZaragozaPersonDeveloperA’Kaia PhelpsPersonDeveloperOna O. IgbinedionPersonDeveloperAhmad R. MersaghianPersonDeveloperIan M. GreenPersonDeveloperLauren L. AmparoPersonDeveloperAlexia M. FillerPersonDeveloperKevin B. PattersonPersonDeveloperJohn L. LopezPersonDeveloperJustin Kyle T. TorresPersonDeveloperEileen ChoePersonDeveloperJen ShinPersonDeveloperMihir SamdarshiPersonDeveloperAnindita VarshneyaPersonDeveloperNicole A. AnguianoPersonDeveloperBritain J. SouthwickPersonDeveloperBen G. FitzpatrickPersonDeveloperLoyola Marymount UniversityInstituteProviderNSF award 0921038; LMU Rains Research Assistant Program; LMU Summer Undergraduate Research ProgramFunding agencyContributorlmu.eduInstituteProviderKam D. Dahlquistkdahlquist@lmu.eduPersonPrimary contactJohn David N. Dionisiodondi@lmu.eduhttps://orcid.org/0000-0001-8655-4693PersonPrimary contact3DBIONOTESWeb based application designed to integrate protein structure, protein sequence and protein annotations in a unique graphical environment. The current version of the application offers a unified, enriched and interactive view of EMDB volumes, PDB structures and Uniprot sequences where the protein annotations stored in Uniprot, Immune Epitope DB, Phospho Site Plus, BioMuta and dSysMap can be explored interactively at sequence and structural level.http://3dbionotes.cnb.csic.es/ws3dbionotesbiotools:3dbionotesv3Database portalhttp://edamontology.org/topic_3366Data integration and warehousinghttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_0078ProteinsWindowsMacLinuxSQLApache-2.0ELIXIR-ESCNB-CSICCOVID-19INBIMPaCT-ISCIIIMatureFree of chargeOpen accessInteroperability3D-BioInfoSpainhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/data_1146EMDB IDhttp://edamontology.org/data_1127PDB IDhttp://edamontology.org/data_3021UniProt accessionIntegration of protein structure, protein sequence and protein annotations in a unique graphical environment.http://3dbionotes.cnb.csic.es/ws/helpGeneral10.1016/j.jsb.2016.02.007Primary10.1093/bioinformatics/btx483Primary10.1093/bioinformatics/btz118Primary10.1093/bioinformatics/btab397PrimaryINBInstituteProviderELIXIR-ESInstituteProvidercnb.csic.esInstituteProviderCarlos Oscar Sorzanocoss@cnb.csic.eshttp://3dbionotes.cnb.csic.eshttps://orcid.org/0000-0002-9473-283XPersonPrimary contactEOSC-LifeFunding agencyEOSC Life [INFRAEOSC-04-2018, Proposal: 824087]CORBELFunding agencyCORBEL [INFRADEV-01-2014-1, Proposal 654248]CSICFunding agencyCSIC [PIE/COVID-19 number 202020E079]Comunidad de MadridFunding agencyComunidad de Madrid through grant CAM [S2017/BMD-3817]Spanish Ministry of Science and InnovationFunding agencySpanish Ministry of Science and Innovation through projects [SEV 2017-0712, FPU-2015/264, PID2019-104757RB-I00/AEI/10.13039/501100011033]Instituto de Salud Carlos IIIFunding agencyInstituto de Salud Carlos III: PT17/0009/0010 [ISCIII-SGEFI/ERDF]BRENDAInternationally leading information system on all aspects of enzymes, including function, structure, involvement in diseases, application, engineering, and molecular properties. The database includes hundreds of milllions of enzyme data and is compiled from manual literature annotation, data integration from other databases and predicted enzyme functions and locations.http://www.brenda-enzymes.orgbrendabiotools:brendaDatabase portalhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3292Biochemistryhttp://edamontology.org/topic_0821Enzymeshttp://edamontology.org/topic_3070Biologyhttp://edamontology.org/topic_3297Biotechnologyhttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_3344Biomedical scienceWindowsMacLinuxCC-BY-4.0de.NBIDSMZ Digital DiversityMatureFree of charge (with restrictions)Open accessDataToolsInteroperabilityGermanyhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3208Genome visualisationhttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/operation_0306Text mininghttp://edamontology.org/operation_2241Transmembrane protein visualisationhttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0269Transmembrane protein predictionhttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_3083Pathway or network visualisationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3194Genome feature comparisonhttp://edamontology.org/operation_0305Literature searchhttp://edamontology.org/data_2909Organism namehttp://edamontology.org/data_0990Compound namehttp://edamontology.org/data_2299Gene namehttp://edamontology.org/data_1127PDB IDhttp://edamontology.org/data_2291UniProt IDhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_2108Reaction IDhttp://edamontology.org/data_2342Pathway or network namehttp://edamontology.org/data_2365Pathway or network accessionhttp://edamontology.org/data_1187PubMed IDhttp://edamontology.org/data_1046Strain namehttp://edamontology.org/data_1179NCBI taxonomy IDhttp://edamontology.org/data_1051Ontology namehttp://edamontology.org/data_1012Enzyme namehttp://edamontology.org/data_1011EC numberhttp://edamontology.org/data_2024Enzyme kinetics data

http://edamontology.org/data_2291UniProt ID

http://edamontology.org/data_1127PDB ID

http://edamontology.org/data_3021UniProt accession

http://edamontology.org/data_2108Reaction ID

http://edamontology.org/data_2342Pathway or network name

http://edamontology.org/data_2365Pathway or network accession

http://edamontology.org/data_1046Strain name

http://edamontology.org/data_2909Organism name

http://edamontology.org/data_1179NCBI taxonomy ID

http://edamontology.org/data_1039SCOP domain identifier

http://edamontology.org/data_2700CATH identifier

http://edamontology.org/data_1012Enzyme name

http://edamontology.org/data_1011EC number

http://edamontology.org/data_2024Enzyme kinetics data

https://www.dsmz.de/Otherhttps://hub.dsmz.de/#/Servicehttps://www.brenda-enzymes.org/Servicehttps://brenda-enzymes.org/support.phpHelpdeskhttp://www.brenda-enzymes.org/copy.phpTerms of usehttp://www.brenda-enzymes.org/introduction.phpCitation instructionshttps://www.brenda-enzymes.org/tutorial.phpTraining materialhttps://www.brenda-enzymes.org/help.phpTraining materialhttps://www.brenda-enzymes.org/faq.phpFAQbtoincludes10.1093/nar/gkaf111341206471PMC12807770Primary10.1093/nar/gkaa102533211880PMC777902010.1093/nar/gky104830395242PMC632394210.1016/j.jbiotec.2017.04.0202843857910.1093/nar/gku106825378310PMC4383907Other10.1093/nar/gkn82018984617PMC2686525Other10.1093/nar/gkq108921062828PMC3013686Other10.1186/1471-2105-12-32921827651PMC3166944Other10.1093/nar/gkh08114681450PMC308815Other10.1093/nar/gks104923203881PMC3531171Other10.1016/s0968-0004(01)02027-811796225Other10.1093/nar/gkl97217202167PMC1899097Other10.1093/nar/30.1.4711752250PMC99121Other10.1093/nar/gkq96821030441PMC3013802OtherBMBFFunding agencyContributorcontact@brenda-enzymes.orgPersonPrimary contactLeibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultureshttps://www.dsmz.de/grid.420081.f02tyer376MADORAA web application for processing and visualization of statistics for bone marrow donors registry - especially statistics of donors, executed searches for suitable donor, the typing and harvests before transplantation.https://cds-madora.zcu.cz/madorabiotools:madora1Web applicationhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3303Medicinehttp://edamontology.org/topic_3342Translational medicineLinuxWindowsMacCzech RepublicELIXIR-CZEmergingCzech Republichttp://edamontology.org/operation_3431Depositionhttp://edamontology.org/operation_0337Visualisation

http://edamontology.org/data_0920Genotype/phenotype reporthttp://edamontology.org/format_2331HTML

Bone marrow donors visualizationhttp://www.kky.zcu.cz/en/sw/madoraTerms of useLucie HoudováPersonDeveloperDaniel GeorgievPersonDeveloperUniversity of West Bohemia, Czech RepublicInstituteProviderELIXIR-CZConsortiumTA CRFunding agencyContributorELIXIR-CZInstituteProviderDaniel Georgievgeorgiev@ntis.zcu.czMaintainerDaniel Georgievgeorgiev@ntis.zcu.czPersonPrimary contactHANAHaplotype analyzer for the Czech population.https://cds-hana.zcu.cz/hanabiotools:hana1Web applicationDesktop applicationhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3303MedicineLinuxWindowsMacCzech RepublicELIXIR-CZEmerginghttp://edamontology.org/operation_0337Visualisation

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_2331HTML

Haplotype analyzerLucie Houdováhoudina@kky.zcu.czPersonDeveloperMiloš Fetterfetter@kky.zcu.czPersonDeveloperDaniel Georgievgeorgiev@kky.zcu.czPersonDeveloperUniversity of West Bohemia, Czech Republichttp://ccy.zcu.czInstituteProviderELIXIR-CZhttps://www.elixir-czech.cz/ConsortiumTA CRhttps://www.tacr.cz/index.php/en/Funding agencyContributorDaniel Georgievgeorgiev@ntis.zcu.czSupportDaniel Georgievgeorgiev@ntis.zcu.czPersonPrimary contactGen SeekerGen Seeker is the browser of variants detected in the Czech population included in the Czech digital genome map. Although Slavs are the largest European ethnolinguistic group, Slavic and especially Czech genomes are underrepresented in international genomic databases, which limits the ability to understand and interpret specific slavic gene variations.https://czechgenome.cz/searchgen_seekerbiotools:gen_seeker1Database portalhttp://edamontology.org/topic_0199Genetic variationMacLinuxWindowsJavaScriptNot licensedELIXIR-CZEATRIS-CZPalacky UniversityRare DiseaseEmergingFree of chargeOpen accessDataHuman Copy Number VariationFederated Human DataRare DiseasesCzech Republichttp://edamontology.org/operation_3918Genome analysishttp://edamontology.org/data_1027Gene ID (NCBI)http://edamontology.org/format_2330Textual formathttp://edamontology.org/data_0860Sequence signature datahttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2012Sequence coordinateshttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_3134Gene transcript reporthttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_3134Gene transcript reporthttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_3752CSV

https://czechgenome.cz/data-infoGeneralInstitute of Applied Biotechnologies, a.s.InstituteDeveloperPalacky University Olomouc, Czech RepublicInstituteMaintainerMinistry of Industry of the Czech RepublicFunding agencyOpen PHACTS Chemistry Registry SystemDatabase of compounds registered in the Open PHACTS platform, with structure similarity search. Look up chemical properties (SMILES).http://ops.rsc.org/open_phacts_chemistry_registry_systembiotools:open_phacts_chemistry_registry_systemDatabase portalhttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_0202Pharmacologyhttp://edamontology.org/topic_2258CheminformaticsMatureFree of chargehttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0360Structural similarity searchhttps://www.openphacts.org/2/sci/contact.htmlHelpdeskhttps://www.openphacts.org/2/sci/terms_and_conditions.htmlTerms of usehttps://www.openphacts.org/2/sci/contact.htmlCitation instructionshttp://support.openphacts.org/support/homeGeneral10.1016/j.drudis.2012.05.01622683805PrimaryRoyal Society of ChemistryInstituteProviderOpen PHACTSConsortiumInnovative Medicines Initiative (IMI)Funding agencyContributorcs.manchester.ac.ukInstituteProviderhttps://www.openphacts.org/2/sci/contact.htmlPersonPrimary 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 contactCABRICommon Access to Biological Resources and Information - A collection of European Biological Resource Centre catalogues.http://www.cabri.org/cabribiotools:cabriDatabase portalhttp://edamontology.org/topic_3339Microbial collectionhttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_3340Cell culture collectionLinuxCUSMI Biological Resources CataloguesMatureFree of chargehttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2597CABRI catalogue namehttp://edamontology.org/data_2380CABRI accession

http://edamontology.org/data_0963Cell line reporthttp://edamontology.org/format_2330Textual format

SRS Standard Interface searchhttp://www.nettab.org/promano/Helpdeskhttp://www.fr.cabri.org/Mirrorhttp://www.be.cabri.org/Mirrorhttp://www.cabri.org/General10.2165/00822942-200594030-0000216231959PrimaryDomenico MarraPersonDeveloperBrendan VaughanPersonDeveloperFrancesca PiersigilliPersonDeveloperLouis RechaussatContributorManfred KrachtContributorGerrit StegehuisContributorHerbert MilchContributorLouis JonesContributorBeatrice DutertreContributorFrancois GuissartContributorCommon Access to Biological Resources and Information (CABRI), EU 5th FP (1996-1999)Funding agencyContributorUSMIInstituteProviderPaolo Romanopaolo.romano@hsanmartino.ithttp://www.nettab.org/promano/SupportPaolo Romanopaolo.romano@hsanmartino.ithttp://www.nettab.org/promano/PersonPrimary contactAquariaSimplifying the generation of insight from protein structures through structure visualisation, annotated with protein features; loads sequence-to-structure alignments from the PSSH2 database, sequence features from UniProt and Interpro and user defined features on demand from JSON files; there is also a WebAPI (see ...).http://aquaria.wsaquariabiotools:aquaria1Web APIWeb applicationhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_2814Protein structure analysisLinuxWindowsMacJavaScriptJavaGPL-2.0Odonoghuelab toolsRostlab toolsMatureFree of chargehttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_1063Sequence identifierhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1869Organism identifierhttp://edamontology.org/format_2330Textual formatYou can find sequences based on a keyword search. For the identified sequence, Aquaria retrieves sequence-to-structure alignments from the PSSH2 database and visualises those on the web page. At the same time, a selected alignment is visualised in the 3D viewer (by default the one with most identical residues between sequence and structure). accession number, ID or part of the name or alias from UniProt Organism names used in UniProt; Homo sapiens used by defaulthttp://edamontology.org/operation_0474Protein structure predictionhttp://edamontology.org/data_1096Sequence accession (protein)http://edamontology.org/format_1963UniProtKB format

http://edamontology.org/data_0893Sequence-structure alignmenthttp://edamontology.org/format_3464JSON

web service to get matching structures with alignment data for a given protein sequence Uniprot accession of query protein glued into the query URL: aquaria.ws/<UniprotAcc>.json json representation of one or more sequence-to-structure alignments annotated with alignment statisticshttps://github.com/ODonoghueLab/AquariaRepositoryhttp://aquaria.ws/help/Aquaria3D_QR_v1.pdfSource codehttp://aquaria.ws/help/Aquaria3D_QR_v1.pdfBinarieshttps://www.youtube.com/watch?v=FAQ3yVGYSzY&feature=youtu.beGeneral10.1038/nmeth.325825633501PrimaryChristian StoltePersonDeveloperKenneth S SabirPersonDeveloperSeán I O'DonoghuePersonDeveloperAndrea SchafferhansPersonDeveloperNelson PerdigãoContributorBurkhard RostContributorVivian HoContributorManfred RoosContributorBenjamin WellmannContributorJulian HeinrichContributorMaria KalemanovContributorFabian A BuskeContributorDepartment for Bioinformatics and Computational Biology, Technische Universität MünchenInstituteProviderDivision of Genomics and Epigenetics, Garvan Institute of Medical Research, SydneyInstituteProviderDigital Productivity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), SydneyInstituteProviderSchool of Molecular Bioscience, The University of SydneyInstituteProviderAmazon AWSConsortiumCSIRO's OCE Science Leader program and its Computational and Simulation Sciences platformFunding agencyContributorAlexander von Humboldt FoundationFunding agencyContributorRostLabInstituteProviderSeán I. O'Donoghuesean@odonoghuelab.orgSupportAndrea Schafferhansandrea.schafferhans@rostlab.orgSupportSeán O'Donoghuesean@odonoghuelab.orgPersonPrimary contactAndrea Schafferhansandrea.schafferhans@rostlab.orgPersonPrimary contactLocTree3Prediction of protein subcellular localization in 18 classes for eukaryota, 6 for bacteria and 3 for archaea.https://rostlab.org/services/loctree3/loctree3biotools:loctree31.0.8Command-line toolWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0123Protein propertieshttp://edamontology.org/topic_2229Cell biologyLinuxPHPJavaPerlJavaScriptGPL-3.0Rostlab toolsPredictProteinMatureFree of chargehttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTA

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

Prediction of protein sucellular localization in 18 classes for eukaryota, 6 classes for bacteria and 3 for archaea using homology searches (PSI-BLAST) and machine learning (SVM) User can provide one or more sequences in FASTA format The prediction output contains: prediction score, from 1 (weak prediction) to 100 (strong prediction); one of 18 localization classes for eukaryota, 6 for bacteria and 3 for archaea; GO identifier; GO term; prediction source (PSI-BLAST or SVM)https://rostlab.org/owiki/index.php/PackagesRepositoryhttps://rostlab.org/owiki/index.php/PackagesSource codehttps://rostlab.org/owiki/index.php/PackagesBinarieshttps://rostlab.org/owiki/index.php/Loctree3General10.1093/nar/gku39624848019PMC4086075Primary10.1093/bioinformatics/bts39022962467PMC3436817OtherMaximilian HechtPersonDeveloperGuy YachdavPersonDeveloperTimothy KarlPersonDeveloperTobias HampPersonDeveloperTatyana GoldbergPersonDeveloperBurkhard RostContributorHenrik NielsenContributorTechnische Universität MünchenInstituteProviderAlexander von Humboldt Foundation through German Federal Ministry for Education and ResearchFunding agencyContributorErnst Ludwig Ehrlich StudienwerkFunding agencyContributorRostLabInstituteProviderlocalization@rostlab.orghttps://rostlab.org/services/loctree3/PersonPrimary contactREMSTool that enables a researcher to submit and a Data Access Committee to process Data Access Applications to sensitive datasets.http://www.csc.fi/remsremsbiotools:rems1.8Web applicationhttp://edamontology.org/topic_3316Computer sciencehttp://edamontology.org/topic_3571Data governancehttp://edamontology.org/topic_3263Data securityhttp://edamontology.org/topic_3489Database managementLinuxWindowsMacJavaLGPL-3.0MatureFree of chargehttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3760Service managementManaging access rights to sensitive datasets.https://confluence.csc.fi/display/REMS/InstallationSource codehttps://confluence.csc.fi/display/REMS/End+User+ManualGeneral10.1186/s12911-017-0424-628330491PMC5363029ReviewJanne LaurosPersonDeveloperCSC - IT Center for ScienceInstituteProviderELIXIRConsortiumAcademy of Finland, grants 271642 and 263164Funding agencyContributorcsc.fiInstituteProviderrems@csc.fiPersonPrimary contactMotifLabGeneral workbench for analyzing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. It can improve performance of binding site predictions by allowing users to integrate several motif discovery tools, as well as different types of data: phylogenetic conservation, epigenetic marks, DNase hypersensitive sites, ChIP-Seq data, positional binding preferences of transcription factors, TF-TF interactions, TF-expression and target gene expression.http://www.motiflab.orgmotiflabbiotools:motiflab1.8Command-line toolDesktop applicationWorkbenchhttp://edamontology.org/topic_0204Gene regulationhttp://edamontology.org/topic_0749Transcription factors and regulatory sitesLinuxWindowsMacJavaNeLSELIXIR-NorwaySEQwikiNTNU toolsMatureFree of chargehttp://edamontology.org/operation_0564Sequence visualisationhttp://www.motiflab.org/index.php?page=downloadRepositoryhttp://www.motiflab.org/index.php?page=contactHelpdeskhttp://www.motiflab.org/MotifLab_source.zipSource codehttp://www.motiflab.org/index.php?page=downloadBinarieshttp://www.motiflab.org/index.php?page=publicationsCitation instructionshttp://www.motiflab.org/index.php?page=documentationGeneral10.1186/1471-2105-14-923323883PMC3556059Primary10.1093/bioinformatics/btq35720628076PMC2922893OtherKjetil KlepperPersonDeveloperFinn DrabløsContributorELIXIR-NorwayConsortiumNeLS (Norwegian e-Infrastructure for Life Sciences)ConsortiumThe National Programme for Research in Functional Genomics in NorwayFunding agencyContributorNorwegian infrastructure for bioinformatics ELIXIR.noFunding agencyContributorNTNUInstituteProviderKjetil Klepperkjetil.klepper@ntnu.nohttp://www.motiflab.org/index.php?page=contactMaintainerFinn Drabløsfinn.drablos@ntnu.nohttp://www.motiflab.org/index.php?page=contactSupportKjetil Klepperkjetil.klepper@ntnu.nohttp://www.motiflab.org/index.php?page=contactPersonPrimary contactFinn Drabløsfinn.drablos@ntnu.nohttp://www.motiflab.org/index.php?page=contactPersonPrimary contactOpen PHACTS ExplorerInterface to the Open PHACTS Discovery Platform and is built to answer the critical pharmacology questions defined by eight major pharmaceutical companies.http://www.openphacts.org/exploreropen_phacts_explorerbiotools:open_phacts_explorer1.5.0Web applicationhttp://edamontology.org/topic_0202Pharmacologyhttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/topic_3336Drug discoveryLinuxWindowsMacRubyMITMatureFree of chargehttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0337Visualisationhttp://github.com/openphacts/explorer2Repositoryhttp://support.openphacts.org/support/homeHelpdeskhttp://iandunlop.eculture.labs.vu.nl/Mirrorhttp://github.com/openphacts/explorer2Source codehttps://www.openphacts.org/terms-and-conditionsTerms of usehttp://ceur-ws.org/Vol-1114/Demo_Dunlop.pdfCitation instructionshttp://support.openphacts.org/support/homeGeneral10.1016/j.drudis.2012.05.01622683805PrimaryIan DunlopPersonDeveloperUniversity of ManchesterInstituteProviderOpen PHACTS FoundationInstituteProviderOpen PHACTSConsortiumInnovative Medicines Initiative (IMI)Funding agencyContributorcs.manchester.ac.ukInstituteProviderOpen PHACTS Explorer issue trackerhttps://github.com/openphacts/explorer2/issuesSupportOpen PHACTS support portalhttp://support.openphacts.org/support/homePersonPrimary contactOpen PHACTS Explorer issue trackerhttps://github.com/openphacts/explorer2/issuesPersonPrimary contactCNOGproDetect and quantify CNVs in prokaryotic whole-genome sequencing data. After aligning WGS reads to a reference genome, we count the individual reads in a sliding window and normalize these counts for bias introduced by differences in GC content.https://cran.r-project.org/web/packages/CNOGpro/index.htmlcnogprobiotools:cnogpro1.1Command-line toolhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0199Genetic variationLinuxWindowsMacRGPL-2.0MatureFree of chargehttp://edamontology.org/operation_3208Genome visualisationhttp://edamontology.org/operation_3233Copy number estimationThe input file (hitsfile) can be constructed from a SAM/BAM filehttps://cran.r-project.org/web/packages/CNOGpro/index.htmlSource codehttp://bioinformatics.oxfordjournals.org/content/31/11/1708.longCitation instructionshttps://cran.r-project.org/web/packages/CNOGpro/index.htmlGeneral10.1093/bioinformatics/btv07025644268PrimaryOla BrynildsrudPersonDeveloperLars-Gustav SnipenPersonDeveloperNorwegian University of Life SciencesInstituteProviderRConsortiumNorwegian University of Life SciencesFunding agencyContributorUiOInstituteProviderola.brynildsrud@nmbu.noPersonPrimary contactStitchprofilesWeb-based computations on DNA melting, thus predicting the localized separation of the two strands for sequences provided by the users.http://stitchprofiles.uio.no/stitchprofilesbiotools:stitchprofiles1Web applicationhttp://edamontology.org/topic_0654DNALinuxWindowsMacMatureFree of chargehttp://edamontology.org/operation_0456Nucleic acid melting profile plottinghttp://edamontology.org/operation_0262Nucleic acid property calculationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2958Nucleic acid melting curvehttp://edamontology.org/format_2330Textual format

melting curves, probability profiles and temperature profiles Maximum sequence length: 140000 bp melting curves, probability profiles and temperature profileshttp://nar.oxfordjournals.org/cgi/content/full/33/suppl_2/W573Citation instructionshttp://stitchprofiles.uio.no/help.phpGeneral10.1093/nar/gki42415980539PMC1160185PrimaryGeir Ivar JerstadPersonDeveloperEivind HovigPersonDeveloperEivind TøstesenPersonDeveloperUniversity of OsloInstituteProviderThe Norwegian Radium HospitalInstituteProviderThe Research Council of NorwayFunding agencyContributorUiOInstituteProviderEivind Hovigehovig@ifi.uio.noPersonPrimary contactCoremine MedicalThis library is ideal for those seeking an overview of a complex subject while allowing the possibility to "drill down" to specific details. Search results are presented in a dashboard format comprised of panels containing various categories of information ranging from introductory sources to the latest scientific articles.http://www.coremine.com/medicalcoremine_medicalbiotools:coremine_medical1Libraryhttp://edamontology.org/topic_3303Medicinehttp://edamontology.org/topic_3070BiologyLinuxWindowsMacMaturehttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_0305Literature searchhttp://edamontology.org/data_0968Keywordhttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2526Text datahttp://edamontology.org/format_2331HTML

http://edamontology.org/data_2353Ontology data

http://edamontology.org/data_2093Data reference

http://www.coremine.com/medical/helppages/HelpPages.html#1Terms of usehttp://www.coremine.com/medical/help.html#searchGeneral10.1002/humu.2204926285306PMC5027376Reviewhttp://www.coremine.com/medical/helppages/HelpPages.html#5Funding agencyContributorUiOInstituteProvidersupport@coremine.comPersonPrimary contactDeepBlue Epigenomic Data ServerProvides a central data access hub for large collections of epigenomic data. It organizes the data from different sources using controlled vocabularies and ontologies. The data is stored in our server, where the users can access the data programmatically or by our web interface. It contains a set of commands designed to perform operations on the epigenomic data. Users can execute all operations in a pipeline fashion in the server and transfer only meaningful data.http://deepblue.mpi-inf.mpg.de/deepbluebiotools:deepblueWeb APIWeb applicationDatabase portalhttp://edamontology.org/topic_3173EpigenomicsLinuxWindowsMacRPHPJavaPythonC++JavaScriptPerlGPL-3.0de.NBIHD-HubMatureFree of chargehttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_3436Aggregationhttp://deepblue.mpi-inf.mpg.de/General10.1093/nar/gkw21127084938PMC4987868PrimaryFelipe AlbrechtPersonDeveloperMax Planck Institute for InformaticsInstituteProviderEU grant No. HEALTH-F5-2011-282510 (BLUEPRINT project)Funding agencyContributorGerman Science Ministry Grant No.01KU1216A (DEEP project)Funding agencyContributormpi-inf.mpg.deInstituteProviderFelipe Albrechtfelipe.albrecht@mpi-inf.mpg.deSupportFelipe Albrechtfelipe.albrecht@mpi-inf.mpg.dePersonPrimary contactPDEStrIAnThe database revolves around the protein structure of catalytic PDE domains and the way PDE inhibitors can interact with them. It contains a systematic analysis of all phosphodiesterase (PDE) catalytic domain crystal structures present in the Protein Data Bank (PDB) with a focus on PDE-ligand interactions.http://pdestrian.vu-compmedchem.nlpdestrianbiotools:pdestrianCommand-line toolWeb applicationWeb APIDatabase portalhttp://edamontology.org/topic_3369Chemical biologyhttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/topic_3332Computational chemistryhttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_0209Medicinal chemistryhttp://edamontology.org/topic_3303Medicinehttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_0122Structural genomicsLinuxWindowsMacMatureFree of chargehttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_3282ID mappinghttp://edamontology.org/operation_2492Protein interaction predictionhttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/operation_02973D profile generationhttp://edamontology.org/operation_0295Structure alignmenthttp://edamontology.org/operation_2480Structure analysishttp://edamontology.org/operation_0244Protein flexibility and motion analysishttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_2996Structure classificationhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_2487Protein structure comparisonhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_2554Alignment format (text)

http://edamontology.org/data_2526Text data

http://edamontology.org/data_1712Chemical structure image

http://edamontology.org/data_0954Database cross-mapping

http://edamontology.org/data_2080Database search results

http://edamontology.org/data_0982Molecule identifier

http://edamontology.org/data_0984Molecule name

http://edamontology.org/data_2050Molecular property (general)

http://edamontology.org/data_0906Protein interaction data

http://edamontology.org/data_1461Protein-ligand complex

http://edamontology.org/data_0897Protein property

http://edamontology.org/data_2992Protein structure image

http://edamontology.org/data_1537Protein structure report

http://edamontology.org/data_0893Sequence-structure alignment

http://edamontology.org/data_1463Small molecule structure

http://edamontology.org/data_1481Structure alignment (protein)

http://edamontology.org/data_0890Structural (3D) profile alignment

http://edamontology.org/data_0889Structural profile

http://edamontology.org/data_0888Structure similarity score

http://edamontology.org/data_1498Tanimoto similarity score

Structures of catalytic kinase domains Sequences of catalytic kinase domains (UniProt)http://pdestrian.vu-compmedchem.nl/faq.phpCitation instructionsGeneral10.1021/acs.jmedchem.5b0181326908025PrimaryDivision of Medicinal Chemistry (Vrije Universiteit Amsterdam)PersonDeveloperChris de GraafPersonDeveloperGeorgi K. KanevPersonDeveloperAlbert J. KooistraPersonDeveloperChimed JansenPersonDeveloperRob LeursContributorIwan J.P. de EschContributorVrije Universiteit AmsterdamInstituteProviderEuropean Commission seventh Framework Programme FP7-HEALTH-2013-INNOVATION-1, PDE4NPD (no. 602666)Funding agencyContributorTI Pharma grant T4-302Funding agencyContributorvu.nlInstituteProviderDr. Chris de Graafc.de.graaf@vu.nlhttp://pdestrian.vu-compmedchem.nl/faq.phpPersonPrimary contactDr. Albert J. Kooistraa.j.kooistra@vu.nlPersonPrimary 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 contactAGCOHThe Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer-reviewed internet journal/encyclopaedia/database focused on genes implicated in cancer, cytogenetics and clinical entities in cancer and cancer-prone hereditary diseases. The main goal of the Atlas is to provide review articles that describe complementary topics, namely, genes, genetic abnormalities, histopathology, clinical diagnoses and a large iconography.http://atlasgeneticsoncology.orgatlasgeneticsoncologybiotools:atlasgeneticsoncologyDatabase portalhttp://edamontology.org/topic_3070Biologyhttp://edamontology.org/topic_3303MedicineLinuxPerlCC-BY-NC-ND-2.0MatureFree of chargehttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2080Database search results

http://edamontology.org/data_0971Articlehttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_2330Textual format

Query and retrieval of articles on human Genes, Leukemia, Tumors, Cancer prone diseases and cytogenetic associated abnormailitieshttp://atlasgeneticsoncology.orgGeneral10.1093/nar/gks108223161685PMC3531131Primary10.1093/nar/gkg12612520000PMC165573OtherJL Huret and P DessenPersonDeveloperINIST CNRS, Nancy, FranceConsortiumsee http://atlasgeneticsoncology.orgFunding agencyContributorigr.frInstituteProviderJean-Loup Huretjlhuret@AtlasGeneticsOncology.orgPersonPrimary contactPhilippe Dessendessen@igr.frPersonPrimary contactGWIPS-vizSpecialized ribosome profiling (ribo-seq) browser providing free access to the genomic alignments of ribo-seq reads in conjunction with mRNA-seq controls along with relevant annotation tracks. Based on the UCSC Genome Browser, the tool’s ribo-seq tracks for various organisms allows for cross-species comparison of orthologous genes while the separate tracks for each ribo-seq study enables cross-study comparisons.http://gwips.ucc.iegwips-vizbiotools:gwips-vizDatabase portalhttp://edamontology.org/topic_0203Gene expressionLinuxWindowsMacMatureFree of chargehttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2495Gene expression analysishttp://gwips.ucc.ie/index.htmlCitation instructionshttp://gwips.ucc.ie/Forum/General10.1093/nar/gkt103524185699PMC3965066Primary10.1002/pmic.20140060325736862PMC4832365OtherMichel AM, Fox G, M Kiran A, De Bo C, O'Connor PB, Heaphy SMPersonDeveloperSchool of Biochemistry & Cell Biology, University College CorkInstituteProviderScience Foundation IrelandFunding agencyContributorucc.ieInstituteProvidergwipsviz@gmail.comhttp://gwips.ucc.ie/PersonPrimary contactGUILDifyUses network-topology based prioritization algorithms in GUILD to score relevance of gene products with respect to given keywords. First, BIANA knowledge base containing data integrated from publicly available major data repositories is queried for gene products associated with the keywords. These gene products are fed to a species-specific interaction network as seed proteins. Finally, a score of relevance for each gene product in the network is calculated by the prioritization algorithm.http://sbi.imim.es/web/GUILDify.phpguildifybiotools:guildify1.0Web APIhttp://edamontology.org/topic_3396Systems medicineLinuxWindowsMachttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/data_2339Ontology concept namehttp://edamontology.org/format_1963UniProtKB format

http://edamontology.org/data_2600Pathway or networkhttp://edamontology.org/format_3619sif

Gene prioritization of genes associated with phenotype and diseases Starting seeds: genes associated with a disease or Keyword(s) of a phenotype or disease Network of associated proteins and drugshttp://sbi.imim.es/web/GUILDify.php/docGeneral10.1093/bioinformatics/btu09224532728Other10.1371/journal.pone.004355723028459PMC3448640OtherEmre Guneyemre.guney@upf.eduhttp://orcid.org/0000-0002-3466-6535PersonDeveloperJavier Garcia-Garciahttp://orcid.org/0000-0001-9539-2606ContributorUPFInstituteProviderMICINN/MINECO & FEBS BIO2011-22568Funding agencyContributorupf.eduInstituteProviderbaldo.oliva@upf.eduPersonPrimary contactRayDe novoassembly of single genomes and metagenomes. Also analyses microbe abundance and performs taxonomic profiling as well as making gene ontology profiling. It can also compare genomic content between samples.http://denovoassembler.sourceforge.netraybiotools:ray2.3.1Command-line toolhttp://edamontology.org/topic_3070BiologyLinuxWindowsMacC++GPL-3.0Debian MedCWLAnimal and Crop GenomicsCloudBioLinuxMatureFree of chargehttp://edamontology.org/operation_0310Sequence assemblyhttps://github.com/sebhtml/rayRepositoryhttp://sebhtml.github.io/Ray.webMirrorhttp://sebhtml.github.io/Ray.web/download.htmlSource codehttp://sebhtml.github.io/Ray.web/download.htmlBinarieshttp://sebhtml.github.io/Ray.web/manual.htmlGeneral10.1186/gb-2012-13-12-r12223259615PMC4056372Primary10.1089/cmb.2009.023820958248PMC3119603OtherSébastien BoisvertPersonDeveloperJacques CorbeilContributorÉlénie GodzaridisContributorFrançois LavioletteContributorFrédéric RaymondContributorInfectious Diseases Research Center, CHUQ Research CenterInstituteProvider1065, av. de la Médecine, Québec (Québec), G1V 0A6, CanadaInstituteProviderFaculty of Medicine, Laval University, 1050, av. de la Médecine, Québec (Québec), G1V 0A6, CanadaInstituteProviderDepartment of Molecular Medicine, Faculty of Medicine, Laval UniversityInstituteProviderCanadian Institutes of Health Research (CIHR), and otherFunding agencyContributorNTNUInstituteProviderAnimesh Sharmasharma.animesh@gmail.comPersonPrimary contactOntology Lookup ServiceRepository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. Users can browse the ontologies through the web interface and programatic access is provided via a RESTful API.http://www.ebi.ac.uk/ols/olsbiotools:ols3Web APIWeb applicationhttp://edamontology.org/topic_0089Ontology and terminologyLinuxWindowsMacJavaScriptJavaApache-2.0MatureInteroperabilityEMBLhttp://edamontology.org/operation_3559Ontology visualisationhttp://edamontology.org/operation_3282ID mappinghttps://github.com/EBISPOT/OLS/Repositoryhttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.ebi.ac.uk/ols/docs/General10.1186/1471-2105-7-9716507094PMC142033510.1093/nar/gkn25218467421PMC244773910.1093/nar/gkq33120460452PMC2896109Simon Jupphttps://www.ebi.ac.uk/~jupp/PersonDeveloperSamples, Phenotypes and Ontologies Teamhttp://www.ebi.ac.uk/about/spot-teamPersonDeveloperEMBL-EBIhttp://www.ebi.ac.ukInstituteProviderElixirhttps://www.elixir-europe.orgConsortiumCORBELhttp://www.corbel-project.eu/home.htmlFunding agencyContributorDIACHRONhttp://www.diachron-fp7.euFunding agencyContributorEMBL-EBIhttp://www.ebi.ac.ukFunding agencyContributorBioMedBridgeshttp://www.biomedbridges.euConsortiumDocumentorebi.ac.ukhttp://www.ebi.ac.ukInstituteProviderOLS GitHubhttps://github.com/EBISPOT/OLSSupportols-support@ebi.ac.ukPersonPrimary contacthttps://github.com/EBISPOT/OLSPersonPrimary contactNorsNetIdentification unstructured loops from sequence.http://ppopen.informatik.tu-muenchen.de/norsnetbiotools:norsnet1.0.16Command-line toolWeb applicationhttp://edamontology.org/topic_2814Protein structure analysisLinuxGPL-2.0Rostlab toolsPredictProteinFree of chargehttp://edamontology.org/operation_0470Protein secondary structure prediction (coils)http://edamontology.org/data_2886Protein sequence record

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

NORSnet is a neural network based method that focuses on the identification of unstructured loops. NORSnet was trained to distinguish between very long contiguous segments with non-regular secondary structure (NORS regions) and well-folded proteins. NORSnet was trained on predicted information rather than on experimental data. Therefore, it was optimized on a large data, which is not biased by today's experimental means of capturing disorder. Thus, NORSnet reached into regions in sequence space that are not covered by the specialized disorder predictors. One disadvantage of this approach is that it is not optimal for the identification of the "average" disordered region. Protein amino-acid sequence in fasta formathttps://rostlab.org/owiki/index.php/PackagesRepositoryhttps://rostlab.org/owiki/index.php/PackagesSource codehttps://rostlab.org/owiki/index.php/PackagesBinarieshttps://rostlab.org/owiki/index.php/NorsnetGeneral10.1371/journal.pcbi.003014017658943PMC1924875PrimaryAvner SchlessingerPersonDeveloperBurkhard RostContributorJinfeng Liuhttp://orcid.org/0000-0002-0343-8222ContributorUniversity of California San DiegoInstituteProviderColumbia UniversityInstituteProviderGrant 2R01-LM07329-01 from the National Library of MedicineFunding agencyContributorRostLabInstituteProviderhelp@predictprotein.orgPersonPrimary contactpEffectPrediction of type III effector proteins from protein sequence.https://rostlab.org/services/peffect/peffectbiotools:peffect0.0.1Command-line toolhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0080Sequence analysisLinuxJavaPerlGPL-2.0Bromberglab toolsRostlab toolsMatureFree of chargehttp://edamontology.org/operation_1777Protein function predictionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_2200FASTA-like (text)

http://edamontology.org/data_1255Sequence featureshttp://edamontology.org/format_3475TSV

Prediction of gram-negative bacterial type III effector proteinshttps://rostlab.org/owiki/index.php/PackagesRepositoryhttps://rostlab.org/owiki/index.php/PackagesSource codehttps://rostlab.org/owiki/index.php/PackagesBinarieshttps://rostlab.org/owiki/index.php/PEffectGeneral10.1038/srep3451627713481PMC5054392PrimaryTatyana GoldbergPersonDeveloperYana BrombergContributorBurkhard RostContributorTechnical University of MunichInstituteProviderRutgers UniversityInstituteProviderAlexander von Humboldt foundation through the German Federal Ministry for Education and ResearchFunding agencyContributorErnst Ludwig Ehrlich StudienwerkFunding agencyContributorRostLabInstituteProviderSupportlocalization@rostlab.orgSupportlocalization@rostlab.orgPersonPrimary contactcropPALA data portal to access the compendium of data on crop protein subcellular locations.http://crop-pal.org/croppalbiotools:croppalDatabase portalhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0780Plant biologyLinuxWindowsMacCC-BY-4.0Proteomicshttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_3646Peptide database searchhttp://crop-pal.org/Terms of usehttp://crop-pal.org/Tutorialv1.2.pdfGeneral10.1093/pcp/pcv17026556651PrimaryARC Centre of Excellence in Plant Energy BiologyInstituteProviderThe University of Western AustraliaInstituteProviderAustralian National Data ServiceFunding agencyContributorunimelb.edu.auInstituteProviderAustraliahttp://www.plantenergy.uwa.edu.au/PersonPrimary contactSWICZA proteomics web database.http://proteom.biomed.cas.cz/swiczbiotools:swiczDatabase portalhttp://edamontology.org/topic_0108Protein expressionhttp://edamontology.org/topic_3520Proteomics experimentWindowsPHPCzech RepublicELIXIR-CZProteomicsMatureFree of charge (with restrictions)DataCzech Republichttp://edamontology.org/operation_2421Database search

http://edamontology.org/data_2531Experiment reporthttp://edamontology.org/format_2331HTML

Database of proteomic time series data for streptomyces, caulobacter and neiseria Interactive form interlinked with other resources as NCBI, SwissProt, KEGGhttp://proteom.biomed.cas.czRepositoryhttp://proteom.biomed.cas.czSource codehttp://proteom.biomed.cas.czBinarieshttp://proteom.biomed.cas.czTerms of useCitation instructionshttp://proteom.biomed.cas.cz/strepto_new/experimental_strep.phpGeneral10.1002/pmic.20030055914625849Other10.1002/pmic.20050020616400688OtherIvan JandaPersonDeveloperJiří­ VohradskýPersonDeveloperJan BobekContributorUrs JenalContributorKarel MikulikContributorMarek BaslerContributorBjorn GrunenfelderContributorInstitute of Microbiology, Prague, Czech RepublicInstituteProviderBiozentrum, Univ. Basel, SwitzerlandInstituteProviderELIXIR-CZConsortiumCzech Science FoundationFunding agencyContributorELIXIR-CZInstituteProviderJiří­ Vohradskývohr@biomed.cas.czSupportJiří Vohradskývohr@biomed.cas.czPersonPrimary contactCocoa Genome HubThe Cocoa Genome Hub is an integrated web-based database providing centralized access to the cocoa reference genome sequences and genomic resources.https://cocoa-genome-hub.southgreen.fr/Cocoa_Genome_Hubbiotools:Cocoa_Genome_HubDatabase portalhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3810Agricultural sciencehttp://edamontology.org/topic_0203Gene expressionLinuxPHPJavaScriptGPL-2.0Genome Hubelixir-fr-sdp-2019MatureFree of chargeDataToolsFrancehttp://edamontology.org/operation_3184Sequence assembly visualisationhttp://edamontology.org/operation_3559Ontology visualisationhttp://edamontology.org/operation_0292Sequence alignmenthttps://cocoa-genome-hub.southgreen.fr/contactHelpdeskhttp://api.tripal.info/api/tripal/3.xAPI documentationhttps://cocoa-genome-hub.southgreen.fr/content/terms-serviceTerms of usesouthgreenincludedIntripalusesjbrowseuses10.1186/s12864-017-4120-928915793PMC5603072Primary10.1038/ng.73621186351Argoutxavier.argout@cirad.frhttps://orcid.org/0000-0002-0100-5511PersonPrimary contactDrocgaetan.droc@cirad.frhttps://orcid.org/0000-0003-1849-1269PersonPrimary contactLanaudclaire.lanaud@cirad.frhttps://orcid.org/0000-0001-6411-7310PersonContributorCIRADhttps://www.cirad.frInstituteMaintainerANRFunding agencyRepeatExplorerRepeatExplorer is a computational pipeline designed to identify and characterize repetitive DNA elements in next-generation sequencing data from plant and animal genomes. It employs graph-based clustering of sequence reads to identify repetitive elements and several additional programs that aid in their annotation and quantification.http://repeatexplorer.orgrepeat_explorerbiotools:repeat_explorer2.3.7 (Galaxy server)0.3.7 (command line)Command-line toolWeb applicationhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_0798Mobile genetic elementsLinuxRPerlPythonGPL-3.0Czech RepublicELIXIR-CZMatureFree of chargeToolsCzech Republichttp://edamontology.org/operation_0379Repeat sequence detectionhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0857Sequence search resultshttp://edamontology.org/format_2310FASTA-HTML

Computational pipeline for discovery and characterization of repetitive sequences in eukaryotic genomes. The pipeline uses high-throughput genome sequencing data as an input and performs graph-based clustering analysis of sequence read similarities to identify repetitive elements within analyzed samples User-provided shotgun sequencing data Characterization of repetitive sequenceshttps://bitbucket.org/petrnovak/repex_tareanRepositoryhttps://repeatexplorer-elixir.cerit-sc.cz/Galaxy servicehttps://bitbucket.org/petrnovak/repex_tareanSource codehttps://bitbucket.org/petrnovak/repex_tareanBinarieshttps://toolshed.g2.bx.psu.edu/view/petr-novak/repeatexplorer2Software packageGalaxy toolshed packagehttp://repeatexplorer.orgTerms of useCitation instructionsGeneralUser manual10.1186/1471-2105-11-37820633259PMC2912890Primary10.1093/bioinformatics/btt05423376349Jiri MacasPersonDeveloperPavel NeumannPersonDeveloperPetr NovakPersonDeveloperBiology Centre, CAS, Czech RepublicInstituteProviderELIXIR-CZConsortiumCzech Academy of SciencesFunding agencyContributorELIXIR-CZInstituteProviderPetr Novakpetr@umbr.cas.czSupportPetr Novakpetr@umbr.cas.czPersonPrimary contactJPhyloIOAn open source Java library for reading and writing various tree and alignment formats. Application developers are able to implement format-independent data processing by including event based readers via the abstract strategy pattern. All readers are designed to deal with large amounts of data (alignments with many and/or very long sequences, large trees) without using a great amount of resources (CPU or RAM).http://bioinfweb.info/JPhyloIO/jphyloiobiotools:jphyloio0.5.4Libraryhttp://edamontology.org/topic_3070Biologyhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_3307Computational biologyLinuxWindowsMacJavaLGPL-3.0EmergingFree of chargeOpen accesshttp://edamontology.org/operation_1812Loadinghttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3357Format detectionhttp://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_1912Nexus formathttp://edamontology.org/format_3159phyloXMLhttp://edamontology.org/format_3160NeXMLhttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_1912Nexus formathttp://edamontology.org/format_3159phyloXMLhttp://edamontology.org/format_1910newickhttp://edamontology.org/format_3160NeXMLhttp://edamontology.org/data_1916Alignmenthttp://edamontology.org/format_1912Nexus formathttp://edamontology.org/format_1991megahttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_2332XMLhttp://edamontology.org/format_3160NeXMLhttp://edamontology.org/format_1997PHYLIP format

http://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_1912Nexus formathttp://edamontology.org/format_3159phyloXMLhttp://edamontology.org/format_3160NeXML

http://edamontology.org/data_1916Alignmenthttp://edamontology.org/format_1912Nexus formathttp://edamontology.org/format_3160NeXMLhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1912Nexus formathttp://edamontology.org/format_3159phyloXMLhttp://edamontology.org/format_1910newickhttp://edamontology.org/format_3160NeXML

Input of type "XML" for phylogenetic trees refers to "XTG" (http://bioinfweb.info/xmlns/xtg ) Input of type XML for alignment refers to "PDE" the alignment formats of PhyDE (http://phyde.de/ )https://twitter.com/bioinfwebSocial mediahttps://github.com/bioinfweb/JPhyloIORepositoryhttp://bioinfweb.info/Code/sventon/repos/JPhyloIO/list/Repositoryhttp://bioinfweb.info/JPhyloIO/DownloadSoftware packagehttp://bioinfweb.info/JPhyloIO/DownloadSoftware packagehttp://bioinfweb.info/JPhyloIO/DownloadAPI specificationhttp://bioinfweb.info/JPhyloIO/DocumentationGeneralhttp://bioinfweb.info/JPhyloIO/Documentation/API/Latest/API documentationhttp://bioinfweb.info/JPhyloIO/Documentation/DemosTraining materialhttp://bioinfweb.info/JPhyloIO/LicenseTerms of use10.1093/database/bav09426424081PMC4589695OtherBen C. Stöverhttp://bioinfweb.info/People/StoeverPersonDeveloperSarah Wiecherswiechers@bioinfweb.infoPersonDeveloperKai F. Müllerkaimueller@uni-muenster.dePersonContributorbioinfwebhttp://bioinfweb.info/ProjectMaintainerDFG (German Research Foundation)http://www.dfg.de/Funding agencyBen C. Stöverhttp://bioinfweb.info/People/StoeverPersonPrimary contactOpen PHACTS APIOpen PHACTS Discovery Platform brings together data from multiple publicly available sources of pharmacological and physicochemical information, in order to streamline research and drug discovery processes. The data is integrated into a consolidated triple store, which can be accessed via applications or workflow tools which make use of the Open PHACTS API.https://dev.openphacts.org/docs/2.1open_phacts_apibiotools:open_phacts_api2.1Web APIhttp://edamontology.org/topic_3343Compound libraries and screeninghttp://edamontology.org/topic_3332Computational chemistryhttp://edamontology.org/topic_3336Drug discoveryLinuxWindowsMacCC-BY-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0360Structural similarity searchhttp://github.com/openphacts/Repositoryhttp://support.openphacts.org/support/homeHelpdeskhttp://data.openphacts.org/Source codehttps://github.com/openphacts/ops-dockerContainer fileDocker Compose setuphttps://www.openphacts.org/2/sci/data.htmlTerms of usehttps://dev.openphacts.org/contactCitation instructionshttps://dev.openphacts.org/docs/2.0General10.3233/SW-2012-0088Other10.1016/j.drudis.2012.05.01622683805OtherOpen PHACTS FoundationInstituteProviderOpenLink SoftwareConsortiumInnovative Medicines Initiative (IMI)Funding agencyContributorcs.manchester.ac.ukInstituteProviderOpen PHACTS contacthttps://dev.openphacts.org/contactPersonPrimary contactOpen PHACTS support portalsupport@openphacts.orghttp://support.openphacts.org/support/homePersonPrimary contactBanana Genome HubA Next-Generation Information System for Musa genomicshttps://banana-genome-hub.southgreen.fr/Banana_Genome_Hubbiotools:Banana_Genome_Hubv2Database portalhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3810Agricultural sciencehttp://edamontology.org/topic_0797Comparative genomicsPHPJavaScriptGPL-2.0Genome Hubelixir-fr-sdp-2019MatureFree of chargeOpen accessToolsDataFrancehttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_3208Genome visualisationhttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_0968Keywordhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_0863Sequence alignment

http://edamontology.org/data_2044Sequence

https://banana-genome-hub.southgreen.fr/contactHelpdeskMailing listhttps://github.com/SouthGreenPlatform/genomehubsIssue trackerhttps://banana-genome-hub.southgreen.fr/downloadBiological datahttps://banana-genome-hub.southgreen.fr/termofservicesTerms of usehttp://api.tripal.info/api/tripal/2.xAPI documentationhttps://banana-genome-hub.southgreen.fr/documentationGeneralsouthgreenincludedIntripaluses10.1093/database/bat03523707967PMC366286510.1038/nature1124122801500Gaëtan Drocgaetan.droc@cirad.frhttps://orcid.org/0000-0003-1849-1269PersonDeveloperMathieu Rouardm.rouard@cgiar.orghttps://orcid.org/0000-0003-1849-1269PersonPrimary contactCIRADInstituteMaintainerBioversity InternationalInstituteANRFunding agencyOcean Gene AtlasThe Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping sequence reads onto gene catalogs). User queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive maps and plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/Ocean_Gene_Atlasbiotools:Ocean_Gene_AtlasDatabase portalhttp://edamontology.org/topic_0610Ecologyhttp://edamontology.org/topic_3387Marine biologyhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3941MetatranscriptomicsPHPJavaScriptNot licensedelixir-fr-sdp-2019MatureFree of chargeOpen accessToolsFrancehttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/operation_0573Map drawinghttp://edamontology.org/operation_3478Phylogenetic tree reconstructionhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1364Hidden Markov modelhttp://edamontology.org/format_1370HMMER formathttp://edamontology.org/data_1138Pfam accession numberhttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2295Gene IDhttp://edamontology.org/format_2330Textual format

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

http://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTA

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

http://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newick

http://edamontology.org/data_0857Sequence search resultshttp://edamontology.org/format_1333BLAST results

http://edamontology.org/data_3736Ecological datahttp://edamontology.org/format_3752CSV

http://edamontology.org/data_2884Plothttp://edamontology.org/format_2331HTML

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3603PNGhttp://edamontology.org/format_3579JPGhttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_3508PDF

http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/build/pdf/Ocean-Gene-Atlas_User_Manual.pdfUser manualAPI documentationhttp://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/termsOfUseTerms of useblastusesmafftusestrimalusesnewick_utilitiesuseshmmer3usesfasttreeuseskronauses10.1093/nar/gky37629788376PMC6030836Primaryoceangeneatlas@mio.osupytheas.frhttp://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/creditsPersonPrimary contactMIOhttps://www.mio.osupytheas.fr/InstituteProviderOCEANOMICShttp://www.oceanomics.eu/Funding agencyANR-11-BTBR-0008MSAViewerLarge MSAs visualization interactively on the web.http://msa.biojs.netmsaviewerbiotools:msaviewer1.0.0Libraryhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxWindowsMacJavaScriptApache-2.0Rostlab toolsBioJSMatureFree 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.https://github.com/wilzbach/msaRepositoryhttp://biojs.io/Software cataloguehttp://github.com/wilzbach/msaHelpdeskhttps://github.com/wilzbach/msaSource codehttps://cdn.bio.sh/Binarieshttps://github.com/wilzbach/msa/blob/master/LICENSETerms of usehttp://msa.biojs.netGeneral10.1093/bioinformatics/btw47427412096PMC5181560PrimarySebastian WilzbachPersonDeveloperIan SillitoeContributorGuy YachdavContributorBenedikt RauscherContributorTatyana GoldbergContributorTechnische Universität MünchenInstituteProviderGoogle Summer of Code (GSoC) 2014Funding agencyContributorBioJSInstituteProviderhttp://github.com/wilzbach/msaPersonPrimary contactMOLEonlineProvides a direct access to MOLE functionality and enables on-line and easy-to-use interactive channel analysis.https://mole.upol.cz/moleonlinebiotools:moleonline3.0Web applicationhttp://edamontology.org/topic_0123Protein propertieshttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0821Enzymeshttp://edamontology.org/topic_0820Membrane and lipoproteinshttp://edamontology.org/topic_0166Protein structural motifs and surfacesLinuxWindowsMacJavaScriptC#CC-BY-NC-3.0LCC NCBRCzech RepublicMOLEELIXIR-CZMatureFree of chargeOpen accessTools3D-BioInfoCzech Republichttp://edamontology.org/operation_0245Protein structural motif recognitionhttp://edamontology.org/operation_1816Surface renderinghttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_2241Transmembrane protein visualisationhttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1477mmCIFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1127PDB IDhttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1539Protein structural quality reporthttp://edamontology.org/format_2331HTML

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1475PDB database entry formathttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_1476PDB

Identification of channels, tunnels, voids and pores within PDB structure. User-prepared PDB file Either PDB file or structural assemblies Interactive visualisation Annotated PDB file with calculated channelshttp://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_manual.pdfRepositoryhttp://webchem.ncbr.muni.cz/Platform/App/MoleMirrorhttps://webchem.ncbr.muni.cz/Platform/AppsBin/Mole/2.5.17.4.24/Mole2_cmd.zipBinarieshttps://mole.upol.cz/aboutTerms of usehttp://mole.upol.cz/aboutCitation instructionshttp://mole.upol.cz/documentation/General10.1093/nar/gks36322553366PMC3394309Primary10.1093/nar/gky30929718451PMC6030847David Sehnaldavid.sehnal@upol.czPersonDeveloperMichal OtyepkaPersonDeveloperOndřej HanákPersonDeveloperKarel BerkaPersonDeveloperCrina-Maria IonescuContributorDeepti JaiswalContributorPavel BanášContributorJaroslav KočaContributorVeronika NavrátilováContributorRadka Svobodová VařekováContributorMasaryk University Brno, Czech RepublicInstituteProviderPalacký University Olomouc, Czech RepublicInstituteProviderELIXIR-CZConsortiumCEITECConsortiumCzech Science foundationFunding agencyContributorPalacky UniversityFunding agencyContributorEuropean Regional Development FundFunding agencyContributorEuropean Social FundFunding agencyContributorMinistry of Education of the Czech RepublicFunding agencyContributorELIXIR-CZInstituteProviderKarel Berkakarel.berka@upol.czSupportPrimary contactmole@upol.czPersonPrimary contactDavid Sehnaldavid.sehnal@upol.czPersonPrimary contactKarel Berkakarel.berka@upol.czPersonPrimary contactInterMineOpen source data warehouse built specifically for the integration and analysis of complex biological data. It enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding your own data.http://www.intermine.orginterminebiotools:intermine5.0.0Command-line toolWeb applicationWeb APIDatabase portalhttp://edamontology.org/topic_3366Data integration and warehousinghttp://edamontology.org/topic_3325Rare diseasesLinuxMacRRubyJavaPythonJavaScriptPerlLGPL-2.1Rare DiseaseMatureFree of chargeToolsUKhttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/data_1255Sequence featureshttp://edamontology.org/format_2330Textual format

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

https://registry.intermine.orgSoftware cataloguehttp://intermine.orgOtherhttp://github.com/intermine/Source codehttps://repo1.maven.org/maven2/org/intermine/Binarieshttp://intermine.org/im-docsGeneralhttp://intermine.org/intermine-user-docsUser manual10.1093/bioinformatics/bts57723023984PMC3516146Primary10.1093/nar/gku30124753429PMC4086141OtherUniversity of CambridgeInstituteProviderBBSRCFunding agencyContributorWellcome TrustFunding agencyContributorNIHFunding agencyContributorgen.cam.ac.ukInstituteProviderPredictSNP2A consensus classifier that combines five of the top performing tools (CADD, DANN, FATHMM, FunSeq2 and GWAVA) for the evaluation of pathogenic effect of SNPs within the human genome. The obtained results are provided together with annotations extracted from dbSNP, GenBank, Clinvar, OMIM, RegulomeDB, HaploReg, UCSC and Ensembl databases.https://loschmidt.chemi.muni.cz/predictsnp2predictsnp2biotools:predictsnp21.0Web applicationhttp://edamontology.org/topic_3063Medical informaticshttp://edamontology.org/topic_2533DNA mutationhttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_0622GenomicsLinuxWindowsMacJavaScriptJavaProprietaryCzech RepublicRare DiseaseELIXIR-CZMatureFree of charge (with restrictions)Open accessToolsCzech Republichttp://edamontology.org/operation_3672Gene functional annotationhttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3019GVFhttp://edamontology.org/format_3016VCF

http://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3016VCFhttp://edamontology.org/format_3508PDF

VCF file containing scores and PDF file containing scores and database linkshttps://loschmidt.chemi.muni.cz/peg/software/predictsnp2-standalone/Downloads page1.0https://loschmidt.chemi.muni.cz/predictsnp2/docs/userguide.pdfUser manual10.1371/journal.pcbi.100496227224906PMC4880439Primary1.0Jaroslav Bendljaroslav.bendl@gmail.comhttps://orcid.org/0000-0001-9989-2720PersonDeveloperJan Stouracstourac.jan@gmail.comhttps://orcid.org/0000-0003-3139-3700PersonDeveloperSupportMilos Musilxmusil46@stud.fit.vutbr.czhttps://orcid.org/0000-0001-9373-7930PersonDeveloperJan Brezovskybrezovsky@mail.muni.czhttps://orcid.org/0000-0001-9677-5078PersonContributorJiri Damborsky1441@mail.muni.czhttps://orcid.org/0000-0002-7848-8216PersonContributorEric D. WiebenPersonContributorJaroslav Zendulkazendulka@fit.vut.czhttps://orcid.org/0000-0001-8718-7493PersonContributorAntonin Pavelka99207@mail.muni.czPersonDeveloperLoschmidt Laboratorieshttps://loschmidt.chemi.muni.cz/peg/InstituteProviderMasaryk University, Brno, Czech Republichttps://www.muni.cz/InstituteProviderInternational Centre for Clinical Research, Brno, Czech Republichttps://www.fnusa-icrc.org/en/InstituteProviderBrno University of Technology, Brno, Czech Republichttps://www.vutbr.cz/InstituteProviderELIXIR-CZhttps://www.elixir-czech.cz/ConsortiumProviderPredictSNP teampredictsnp@sci.muni.czPersonPrimary contactEuropean Regional Development FundFunding agencyContributorEuropean Social FundFunding agencyContributorGrant Agency of the Czech RepublicFunding agencyContributorMinistry of Education of the Czech RepublicFunding agencyContributorBrno University of TechnologyFunding agencyContributorCaverDockPerforms rapid analysis of transport processes in proteins. It models the transportation of a ligand from outside environment into the protein active or binding site and vice versa. It implements a novel algorithm to produce contiguous ligand trajectory and estimation of a binding energy along the pathway. The current version uses CAVER for pathway identification and heavily modified Autodock Vina as a docking engine.https://loschmidt.chemi.muni.cz/caverdock/caverdockbiotools:caverdock1.01.1Command-line toolhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0078ProteinsLinuxWindowsMacC++PythonProprietaryCAVERELIXIR-CZMatureFree of charge (with restrictions)Tools3D-BioInfoCzech Republichttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1537Protein structure reporthttp://edamontology.org/format_1957rawhttp://edamontology.org/format_1476PDB

trajectory of ligand passing through protein tunnel and its energyhttps://www.fi.muni.cz/~xfilipov/caverdock/caverdock-ubuntu-14.04.tar.gzBinariesv1.0, Ubuntu 14.041.0https://www.fi.muni.cz/~xfilipov/caverdock/caverdock-ubuntu-16.04.tar.gzBinariesv1.0, Ubuntu 16.041.0https://www.fi.muni.cz/~xfilipov/caverdock/caverdock-1.1-ubuntu-16.04.tar.xzBinariesv1.1, Ubuntu 16.041.1https://www.fi.muni.cz/~xfilipov/caverdock/caverdock-1.1-ubuntu-18.04.tar.xzBinariesv1.1, Ubuntu 18.041.1https://www.fi.muni.cz/~xfilipov/caverdock/manual.pdfUser manualversion 1.0https://www.fi.muni.cz/~xfilipov/caverdock/manual-1.1.pdfUser manualversion 1.110.1093/bioinformatics/btz38631077297Primary1.010.1109/tcbb.2019.290749230932844Primary1.0Jiri Filipovicfila@mail.muni.czhttps://orcid.org/0000-0002-5703-9673PersonDeveloperOndrej Vavrao.vavra@mail.muni.czPersonContributorJan Plhak408420@mail.muni.czPersonDeveloperDavid Bednar222755@mail.muni.czhttps://orcid.org/0000-0002-6803-0340PersonContributorSergio Marquessmar96@gmail.comhttps://orcid.org/0000-0002-6281-7505PersonContributorJan Brezovskybrezovsky@mail.muni.czhttps://orcid.org/0000-0001-9677-5078PersonContributorJan Stouracstourac.jan@gmail.comhttps://orcid.org/0000-0003-3139-3700PersonDeveloperSupportLudek MatyskaLudek.Matyska@muni.czhttps://orcid.org/0000-0001-6399-5453PersonContributorJiri Damborsky1441@mail.muni.czhttps://orcid.org/0000-0002-7848-8216PersonContributorLoschmidt Laboratorieshttps://loschmidt.chemi.muni.cz/peg/InstituteProviderMasaryk University, Brno, Czech Republichttps://www.muni.cz/InstituteProviderInternational Centre for Clinical Research, Brno, Czech Republichttps://www.fnusa-icrc.org/en/InstituteProviderELIXIR-CZhttps://www.elixir-czech.cz/ConsortiumProviderCaverDock teamcaver@caver.czPersonPrimary contactEuropean CommissionFunding agencyContributorCzech Science FoundationFunding agencyContributorBrno City MunicipalityFunding agencyContributorCAVER WebA web interface for identification and analysis of tunnels and channels in static protein structures with automated starting point detection.https://loschmidt.chemi.muni.cz/caverweb/caver_webbiotools:caver_web1.1Web applicationhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0078ProteinsLinuxWindowsMacJavaScriptJavaProprietaryCzech RepublicELIXIR-CZCAVERMatureFree of charge (with restrictions)Open accessToolsCzech Republichttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1537Protein structure reporthttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_1476PDB

identification of tunnels and pocketshttps://loschmidt.chemi.muni.cz/caverweb/?action=help&User manualhttps://loschmidt.chemi.muni.cz/caverweb/?action=example&Training materialhttps://loschmidt.chemi.muni.cz/caverweb/?action=terms&Terms of useuniprotkb_swiss-protusesfpocketusescaverusescaverdockuses10.1093/nar/gkz37831114897PMC6602463PrimaryJan Stouracstourac.jan@gmail.comhttps://orcid.org/0000-0003-3139-3700PersonDeveloperSupportOndrej Vavrao.vavra@mail.muni.czPersonContributorPiia Kokkonenpiia@mail.muni.czhttps://orcid.org/0000-0001-6002-1856PersonContributorJiri Filipovicfila@mail.muni.czhttps://orcid.org/0000-0002-5703-9673PersonDeveloperGaspar Pintojosegasparpinto@gmail.comhttps://orcid.org/0000-0002-8917-1169PersonContributorJan Brezovskybrezovsky@mail.muni.czhttps://orcid.org/0000-0001-9677-5078PersonContributorJiri Damborsky1441@mail.muni.czhttps://orcid.org/0000-0002-7848-8216PersonContributorDavid Bednar222755@mail.muni.czhttps://orcid.org/0000-0002-6803-0340PersonContributorMarie Jankujova423826@mail.muni.czhttps://orcid.org/0000-0003-3219-8149PersonDeveloperLoschmidt Laboratorieshttps://loschmidt.chemi.muni.cz/peg/InstituteProviderMasaryk University, Brno, Czech Republichttps://www.muni.cz/InstituteProviderInternational Centre for Clinical Research, Brno, Czech Republichttps://www.fnusa-icrc.org/en/InstituteProviderELIXIR-CZhttps://www.elixir-czech.cz/ConsortiumProviderCAVER teamcaver@caver.czPersonPrimary contactCzech Science FoundationFunding agencyContributorMinistry of Education of the Czech RepublicFunding agencyContributorEuropean UnionFunding agencyContributorCAVER PyMOL pluginA PyMOL plugin for identification and analysis of tunnels and channels in static protein structures.http://www.caver.czcaver_pymol_pluginbiotools:caver_pymol_plugin3.0.3LibraryPlug-inhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0078ProteinsLinuxWindowsMacPythonGPL-3.0Czech RepublicELIXIR-CZCAVERMatureFree of chargehttp://edamontology.org/operation_0250Protein property calculation

http://edamontology.org/data_1537Protein structure reporthttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_1476PDB

Analysis of tunnels and channels in proteinshttps://github.com/loschmidt/caver-pymol-pluginRepositoryhttp://caver.cz/index.php?sid=199Downloads pagehttps://github.com/loschmidt/caver-pymol-plugin/archive/v3.0.3.zipSource code3.0.3http://www.caver.cz/index.php?sid=123Citation instructionshttp://www.caver.cz/index.php?sid=132Generalhttp://www.caver.cz/fil/download/manual/caver_plugin_userguide.pdfUser manualcaveruses10.1371/journal.pcbi.100270823093919PMC3475669PrimaryEva Sebestova40707@mail.muni.czPersonContributorAntonin Pavelka99207@mail.muni.czPersonDeveloperPetr Benes60865@mail.muni.czPersonDeveloperOndrej Strnadondrejstrnad@mail.muni.czhttps://orcid.org/0000-0002-8077-4692PersonDeveloperJan Brezovskybrezovsky@mail.muni.czhttps://orcid.org/0000-0001-9677-5078PersonContributorBarbora Kozlikovakozlikova@mail.muni.czhttps://orcid.org/0000-0003-0045-0872PersonContributorArtur GoraArtur.Gora@polsl.plhttps://orcid.org/0000-0003-2530-6957PersonContributorVilem Sustrsulys@mail.muni.czPersonDeveloperMartin Klvanacontact@martinklvana.comhttps://orcid.org/0000-0002-5076-4936PersonContributorPetr Medekxmedek@mail.muni.czPersonDeveloperLada Biedermannovalada.biedermannova@ibt.cas.czhttps://orcid.org/0000-0001-6504-6403PersonContributorJiri Sochorsochor@fi.muni.czPersonContributorJiri Damborsky1441@mail.muni.czhttps://orcid.org/0000-0002-7848-8216PersonContributorLoschmidt Laboratorieshttps://loschmidt.chemi.muni.cz/peg/InstituteProviderMasaryk University, Brno, Czech Republichttps://www.muni.cz/InstituteProviderInternational Centre for Clinical Research, Brno, Czech Republichttps://www.fnusa-icrc.org/en/InstituteProviderELIXIR-CZhttps://www.elixir-czech.cz/ConsortiumProviderCAVER teamcaver@caver.czPersonPrimary contactCzech Science FoundationFunding agencyContributorMinistry of Education of the Czech RepublicFunding agencyContributorEuropean Regional Development FundFunding agencyContributorGrant Agency of the Czech Academy of SciencesFunding agencyContributorEuropean CommunityFunding agencyContributorSouth Moravian RegionFunding agencyContributorBrno City MunicipalityFunding agencyContributorCAVERA tool for identification and analysis of tunnels and channels in static and dynamic protein structures.http://www.caver.czcaverbiotools:caver3.02Command-line toolhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0078ProteinsLinuxWindowsMacJavaGPL-3.0Czech RepublicELIXIR-CZCAVERMatureFree of chargeOpen accessToolsCzech Republichttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1537Protein structure reporthttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_1476PDB

Analysis of tunnels and channels in proteinshttp://www.caver.cz/fil/download/caver30/302/caver_3.0.2.zipRepositoryhttp://www.caver.cz/fil/download/caver30/302/caver_3.0.2.zipSource codehttp://www.caver.cz/fil/download/caver30/302/caver_3.0.2.zipBinarieshttp://www.caver.cz/index.php?sid=123Citation instructionshttp://www.caver.cz/index.php?sid=132General10.1371/journal.pcbi.100270823093919PMC3475669PrimaryEva Sebestova40707@mail.muni.czPersonContributorAntonin Pavelka99207@mail.muni.czPersonDeveloperPetr Benes60865@mail.muni.czPersonDeveloperOndrej Strnadondrejstrnad@mail.muni.czhttps://orcid.org/0000-0002-8077-4692PersonDeveloperJan Brezovskybrezovsky@mail.muni.czhttps://orcid.org/0000-0001-9677-5078PersonContributorBarbora Kozlikovakozlikova@mail.muni.czhttps://orcid.org/0000-0003-0045-0872PersonContributorArtur GoraArtur.Gora@polsl.plhttps://orcid.org/0000-0003-2530-6957PersonContributorVilem Sustrsulys@mail.muni.czPersonDeveloperMartin Klvanacontact@martinklvana.comhttps://orcid.org/0000-0002-5076-4936PersonContributorPetr Medekxmedek@mail.muni.czPersonDeveloperLada Biedermannovalada.biedermannova@ibt.cas.czhttps://orcid.org/0000-0001-6504-6403PersonContributorJiri Sochorsochor@fi.muni.czPersonContributorJiri Damborsky1441@mail.muni.czhttps://orcid.org/0000-0002-7848-8216PersonContributorLoschmidt Laboratorieshttps://loschmidt.chemi.muni.cz/peg/InstituteProviderMasaryk University, Brno, Czech Republichttps://www.muni.cz/InstituteProviderInternational Centre for Clinical Research, Brno, Czech Republichttps://www.fnusa-icrc.org/en/InstituteProviderELIXIR-CZhttps://www.elixir-czech.cz/ConsortiumProviderCAVER teamcaver@caver.czPersonPrimary contactCzech Science FoundationFunding agencyContributorMinistry of Education of the Czech RepublicFunding agencyContributorEuropean Regional Development FundFunding agencyContributorGrant Agency of the Czech Academy of SciencesFunding agencyContributorEuropean CommunityFunding agencyContributorSouth Moravian RegionFunding agencyContributorBrno City MunicipalityFunding agencyContributorEnzymeMinerEnzymeMiner identifies putative members of enzyme families or subfamilies and facilitates the selection of promising targets for experimental characterization. Two key selection criteria are (i) the predicted solubility and (ii) the sequence identities visualised using an interactive sequence similarity network. The search query can be a sequence from the Swiss-Prot database or a custom sequence with a custom description of essential residues. The output is an interactive selection table containing annotated identified sequences.https://loschmidt.chemi.muni.cz/enzymeminer/enzymeminerbiotools:enzymeminer1.0Web applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_0821Enzymeshttp://edamontology.org/topic_0078ProteinsLinuxWindowsMacJavaScriptJavaProprietaryCzech RepublicELIXIR-CZMatureFree of charge (with restrictions)Open accessToolsCzech Republichttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_0361Sequence annotationhttp://edamontology.org/operation_0409Protein solubility predictionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_3620xlsx

http://edamontology.org/data_1233Sequence set (protein)http://edamontology.org/format_1929FASTA

http://edamontology.org/data_1245Sequence cluster (protein)

https://loschmidt.chemi.muni.cz/enzymeminer/helpUser manualhttps://loschmidt.chemi.muni.cz/enzymeminer/exampleTraining materialhttps://loschmidt.chemi.muni.cz/enzymeminer/terms-of-useTerms of useblastusesusearchusesclustalousestmhmmusesinterproscan_4usessoluprotusesbioprojectusesncbi_taxonomy_databaseusescytoscapeusesmmseqs2usesuniprotkb_swiss-protuses10.1093/nar/gkaa37232392342PMC7319543Jiri Honxhonji01@stud.fit.vutbr.czhttps://orcid.org/0000-0002-3321-9629PersonDeveloperSimeon BorkoPersonDeveloperJan Stouracstourac.jan@gmail.comhttps://orcid.org/0000-0003-3139-3700PersonDeveloperSupportZbynek Prokopzbynek@chemi.muni.czhttps://orcid.org/0000-0001-9358-4081PersonContributorJaroslav Zendulkazendulka@fit.vut.czhttps://orcid.org/0000-0001-8718-7493PersonContributorDavid Bednar222755@mail.muni.czhttps://orcid.org/0000-0002-6803-0340PersonContributorTomas Martinekmartinto@fit.vutbr.czPersonContributorJiri Damborsky1441@mail.muni.czhttps://orcid.org/0000-0002-7848-8216PersonContributorLoschmidt Laboratorieshttps://loschmidt.chemi.muni.cz/peg/InstituteProviderMasaryk University, Brno, Czech Republichttps://www.muni.cz/InstituteProviderInternational Centre for Clinical Research, Brno, Czech Republichttps://www.fnusa-icrc.org/en/InstituteProviderBrno University of Technology, Brno, Czech Republichttps://www.vutbr.cz/InstituteProviderELIXIR-CZhttps://www.elixir-czech.cz/ConsortiumProviderEnzymeMiner teamenzymeminer@sci.muni.czPersonPrimary contactEuropean CommissionFunding agencyContributorCzech Science FoundationFunding agencyContributorMinistry of Education of the Czech RepublicFunding agencyContributorCAVER AnalystA tool for interactive visualization and analysis of tunnels, channels and cavities in protein structures.https://www.caver.czcaver_analystbiotools:caver_analyst2.0Desktop applicationhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0078ProteinsLinuxWindowsMacJavaProprietaryCzech RepublicELIXIR-CZCAVERMatureFree of charge (with restrictions)Open accessToolsCzech Republichttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/operation_0384Accessible surface calculationhttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3881AMBER tophttp://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3875XTChttp://edamontology.org/format_3650NetCDFhttp://edamontology.org/format_3881AMBER tophttp://edamontology.org/format_3910trrhttp://edamontology.org/format_3882PSF

http://edamontology.org/data_1537Protein structure reporthttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_1476PDB

Analysis and visualization of tunnels and channels in proteinshttps://www.caver.cz/fil/download/caver_analyst/caver_analyst2_beta2.zipBinaries2.0https://caver.cz/index.php?sid=199Downloads pagehttp://www.caver.cz/index.php?sid=123Citation instructionshttps://caver.cz/fil/download/manual/CAVER_Analyst_2.0_Beta-user_guide.pdfUser manualcaverusesuniprotkb_swiss-protuses10.1093/bioinformatics/bty38629741570PMC6184705PrimaryAdam Jurcikadikuv@gmail.comPersonDeveloperDavid Bednar222755@mail.muni.czhttps://orcid.org/0000-0002-6803-0340PersonContributorJan Byskabyska@mail.muni.czPersonDeveloperSergio Marquessmar96@gmail.comhttps://orcid.org/0000-0002-6281-7505PersonContributorKatarina Furmanovafurmanova@mail.muni.czPersonDeveloperLukas Daniel211165@mail.muni.czhttps://orcid.org/0000-0003-2502-9224PersonContributorPiia Kokkonenpiia@mail.muni.czhttps://orcid.org/0000-0001-6002-1856PersonContributorJan Brezovskybrezovsky@mail.muni.czhttps://orcid.org/0000-0001-9677-5078PersonContributorOndrej Strnadondrejstrnad@mail.muni.czhttps://orcid.org/0000-0002-8077-4692PersonDeveloperJan Stouracstourac.jan@gmail.comhttps://orcid.org/0000-0003-3139-3700PersonDeveloperSupportAntonin Pavelka99207@mail.muni.czPersonDeveloperMartin Manakmanak@kiv.zcu.czhttps://orcid.org/0000-0002-1248-7042PersonDeveloperJiri Damborsky1441@mail.muni.czhttps://orcid.org/0000-0002-7848-8216PersonContributorBarbora Kozlikovakozlikova@mail.muni.czhttps://orcid.org/0000-0003-0045-0872PersonContributorLoschmidt Laboratorieshttps://loschmidt.chemi.muni.cz/peg/InstituteProviderMasaryk University, Brno, Czech Republichttps://www.muni.cz/InstituteProviderInternational Centre for Clinical Research, Brno, Czech Republichttps://www.fnusa-icrc.org/en/InstituteProviderUniversity of West Bohemia, Plzen, Czech Republichttps://www.zcu.cz/InstituteProviderELIXIR-CZhttps://www.elixir-czech.cz/ConsortiumProviderCAVER teamcaver@caver.czPersonPrimary contactCzech Science FoundationFunding agencyContributorMinistry of Education of the Czech RepublicFunding agencyContributorNorwegian Research CouncilFunding agencyContributorPredictSNPA consensus classifier that combines six of the top performing tools for the prediction of the effects of mutation on protein function. The obtained results are provided together with annotations extracted from the Protein Mutant Database and the UniProt database.https://loschmidt.chemi.muni.cz/predictsnp1predictsnpbiotools:predictsnp1.0Command-line toolWeb applicationhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_3063Medical informaticshttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3053GeneticsLinuxWindowsMacJavaScriptJavaPythonProprietaryCzech RepublicRare DiseaseELIXIR-CZMatureFree of charge (with restrictions)Open accessToolsCzech Republichttp://edamontology.org/operation_0331Variant effect predictionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTA

http://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2291UniProt ID

Prediction of the effect of amino acid substitution on protein functionhttps://loschmidt.chemi.muni.cz/predictsnp1/docs/predictsnp-1.0.tar.gzBinarieshttps://loschmidt.chemi.muni.cz/predictsnp1/docs/USER_GUIDE.pdfUser manualmappusesnssnpanalyzerusespantherusesphd-snpusespolyphenusespolyphen-2usessiftusessnapuses10.1371/journal.pcbi.100344024453961PMC3894168Primary1.0Jaroslav Bendljaroslav.bendl@gmail.comhttps://orcid.org/0000-0001-9989-2720PersonDeveloperJan Stouracstourac.jan@gmail.comhttps://orcid.org/0000-0003-3139-3700PersonDeveloperSupportOndrej SalandaPersonDeveloperJan Brezovskybrezovsky@mail.muni.czhttps://orcid.org/0000-0001-9677-5078PersonContributorJiri Damborsky1441@mail.muni.czhttps://orcid.org/0000-0002-7848-8216PersonContributorEric D. WiebenPersonContributorJaroslav Zendulkazendulka@fit.vut.czhttps://orcid.org/0000-0001-8718-7493PersonContributorAntonin Pavelka99207@mail.muni.czPersonDeveloperLoschmidt Laboratorieshttps://loschmidt.chemi.muni.cz/peg/InstituteProviderMasaryk University, Brno, Czech Republichttps://www.muni.cz/InstituteProviderInternational Centre for Clinical Research, Brno, Czech Republichttps://www.fnusa-icrc.org/en/InstituteProviderBrno University of Technology, Brno, Czech Republichttps://www.vutbr.cz/InstituteProviderMayo Clinic, Rochester, New York, United States of Americahttps://www.mayoclinic.org/InstituteProviderELIXIR-CZhttps://www.elixir-czech.cz/ConsortiumProviderPredictSNP teampredictsnp@sci.muni.czPersonPrimary contactEuropean Regional Development FundFunding agencyContributorEuropean Social FundFunding agencyContributorGrant Agency of the Czech RepublicFunding agencyContributorMinistry of Education of the Czech RepublicFunding agencyContributorBrno University of TechnologyFunding agencyContributorSETTERA web application for RNA structure comparison.http://setter.projekty.ms.mff.cuni.cz/setterbiotools:setter1.0Web applicationhttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_0097Nucleic acid structure analysisLinuxC++PythonCzech RepublicELIXIR-CZMatureFree of chargeToolsCzech Republichttp://edamontology.org/operation_2481Nucleic acid structure analysishttp://edamontology.org/operation_0502RNA secondary structure alignmenthttp://edamontology.org/data_1127PDB IDhttp://edamontology.org/format_1476PDB

http://edamontology.org/data_0881Secondary structure alignment (RNA)

Secondary-based RNA tertiary structure superposition either PDBID or user-prepared PDBhttp://setter.projekty.ms.mff.cuni.cz/help/index/Citation instructionsGeneral10.1093/nar/gks56022693209PMC3394248Primary10.1186/s12859-015-0696-826264783PMC4531852Other10.1109/tcbb.2014.235181026357263OtherPetr ČechPersonDeveloperDavid HokszaPersonDeveloperDaniel SvozilPersonDeveloperDaniel SvozilContributorCharles University in Prague, Czech RepublicInstituteProviderUniversity of Chemistry and Technology Prague, Czech RepublicInstituteProviderELIXIR-CZConsortiumCzech Science FoundationFunding agencyContributorELIXIR-CZInstituteProviderDaniel Svozilsvozild@vscht.czSupportDavid Hokszadavid.hoksza@mff.cuni.czSupportDaniel Svozilsvozild@vscht.czPersonPrimary contactDavid Hokszadavid.hoksza@mff.cuni.czPersonPrimary contactClustal OmegaMultiple sequence alignment software. The name is occassionally spelled as ClustalOmega, Clustal Ω, ClustalΩ, Clustal O, ClustalO.http://www.clustal.org/omega/clustalobiotools:clustalo1.0 - 1.2Command-line toolLibraryhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacGPL-2.0clustalBiocondagalaxyPasteurDebianMedMatureFree of chargeOpen accesshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTA

https://galaxy.pasteur.fr/?tool_id=toolshed.pasteur.fr%2Frepos%2Fdcorreia%2Fclustalo%2Fclustalo%2F1.2.1.1&version=1.2.1.1&__identifer=9si4ugr4fwuGalaxy servicehttp://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustalIssue trackerhttp://www.clustal.org/omega/#DownloadDownloads pagehttps://tracker.debian.org/pkg/clustaloSoftware packageDebian package (Debian Med Packaging Team). Source code package 'clustalo' and binary packages including API and its documentation.https://bioconda.github.io/recipes/clustalo/README.htmlSoftware packageConda package (Bioconda channel). Conda recipe at https://github.com/bioconda/bioconda-recipes/tree/master/recipes/clustalo/meta.yamlhttp://www.clustal.org/omega/#DocumentationGeneralhttp://www.clustal.org/omega/READMEUser manualClustal README filehttp://www.clustal.org/omega/INSTALLInstallation instructions10.1038/msb.2011.7521988835PMC3261699Primary10.1002/pro.329028884485PMC5734385Primary10.1002/0471250953.bi0313s4825501942UsageHow to use Clustal Omega. Not open access.Clustal helpdeskclustalw@ucd.ieDivisionPrimary contactScience Foundation Irelandhttp://www.sfi.ie/Funding agencyCyGenexpiCyGenexpi is a Cytoscape plugin for validating/inferring genetic networks from time series expression data. It is based on a ordinary differential equation (ODE) model of gene regulation.https://github.com/cas-bioinf/genexpi/wiki/CyGenexpiCyGenexpibiotools:CyGenexpi1.4.21.3.0Plug-inhttp://edamontology.org/topic_0204Gene regulationLinuxWindowsMacJavaLGPL-3.0EmergingFree of chargeOpen accessToolsCzech Republichttp://edamontology.org/operation_1781Gene regulatory network analysishttp://edamontology.org/data_3112Gene expression matrixhttp://edamontology.org/format_3751DSV

http://edamontology.org/data_2984Pathway or network reporthttp://edamontology.org/format_3751DSV

More info at https://github.com/cas-bioinf/genexpi/wiki/ExampleUse the menu item Apps -> Genexpi -> Genexpi Wizardhttps://github.com/cas-bioinf/genexpiRepositoryhttp://apps.cytoscape.org/apps/cygenexpiSoftware cataloguehttp://apps.cytoscape.org/apps/cygenexpiDownloads page1.4.2https://github.com/cas-bioinf/genexpiSource code1.4.2https://github.com/cas-bioinf/genexpi/wiki/CyGenexpiGeneral10.1186/s12859-018-2138-x29653518PMC58994121.3.0Martin Modrákmartin.modrak@biomed.cas.czhttp://orcid.org/0000-0002-8886-7797PersonPrimary contactDeveloperMinistry of Education, Youth and Sports of the Czech RepublicFunding agencyC4Sys research infrastructure project (MEYS project No: LM20150055), and ELIXIR_CZ project (MEYS project no. LM2015047)