MicroMinerMicroMiner assists in identifying single-residue substitutions in protein structure databases. It searches protein residue environments with local sequence and structural similarity based on the SIENA methodology. Users can search for structural mutation in the entire PDB, their in-house structure collection, or (subsets of) the AlphaFold Database. They can use the method to explore the mutation landscape of proteins with experimental or predicted structures. MicroMiner can be applied to single domains or even protein-protein or protein-ligand interfaces. Several filter options to simplify downstream analysis are available.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/microminer.htmlmicrominerbiotools:microminerCommand-line toolWeb servicehttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_0091BioinformaticsMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFstructural single-residue substitution search and analysishttps://proteins.plusServiceA web service to run MicroMiner calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneralsienauses10.1093/bib/bbad357PrimaryProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderProteinsPlusThe ProteinsPlus web server aims to support life scientists in working with protein structures. Protein structures are the key to understanding protein function. They are an important resource in many biotechnological application areas from pharmaceutical research to biocatalysis. ProteinsPlus focuses on protein-ligand interactions. The server provides support for the initial steps of dealing with protein structures, namely structure search, quality assessment, and preprocessing. JAMDA enables users to perform an on-the-fly molecular docking of up to five molecules. The poses can then be visualized in 2D (PoseView, PoseEdit). Furthermore, advanced options, such as protein pocket detection (DoGSite), prediction of water molecule positions (WarPP), protein structure ensemble generation (SIENA), prediction of metal coordination (METALizer), the analysis of solvent channels in protein crystals (LifeSoaks), or the categorization of protein-protein-interfaces (HyPPI) are supported.https://proteins.plusproteinsplusbiotools:proteinsplusWeb serviceWeb APIhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3534Protein binding sitesLinuxWindowsMacOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFprediction of protonation states and tautomers and placement of hydrogen atomshttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_1844Protein geometry validationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFquality profiling for protein-ligand complexeshttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0384Accessible surface calculationhttp://edamontology.org/operation_2480Structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFcalculating bottleneck radii for crystal solvent channelshttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFatom-level assessment of the electron density fit for structures solved by X-ray crystallographyhttp://edamontology.org/operation_2949Protein-protein interaction analysishttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBprotein-protein interface classification (permanent, transient, crystal artifact)http://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_1197InChIhttp://edamontology.org/format_1196SMILEShttp://edamontology.org/format_3816Mol2http://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFprotein-ligand docking for small moleculeshttp://edamontology.org/operation_3897Ligand-binding site predictionhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFsmall molecule binding site detectionhttp://edamontology.org/operation_3897Ligand-binding site predictionhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFsmall molecule binding site detection and druggability assessmenthttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF2D interaction diagram drawing and editinghttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFmetal complex geometry predictionhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF2D interaction diagram drawinghttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFstructural single-residue substitution search and analysishttp://edamontology.org/operation_2844Structure clusteringhttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFPDB mining and protein binding site ensemble generationhttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0306Text mininghttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFtextual, numerical, and chemical 3D searches in the PDBhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFwater molecule placementhttps://proteins.plusServicehttps://proteins.plus/help/indexGeneraldogsitescorerincludesdogsite3includesediaincludessienaincludesmetalizerincludesstructureprofilerincludesjamdaincludesgeomineincludesmicrominerincludesposeeditincludesposeviewincludesprotossincludeslifesoaksincludesppiincludes10.1093/nar/gkx33328472372PMC5570178Primary10.1093/nar/gkaa23532297936PMC7319454Usage10.1093/nar/gkac30535489057PMC9252762Usage10.1093/nar/gkaf37740326518PMC12230695UsageProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderJAMDAJAMDA enables the preparation of individual protein structures and the docking of small molecules in preprocessed binding sites of choice. JAMDA simplifies the process of protein-ligand docking by automatic preprocessing protocols for the protein and binding sites of interest. The JAMDAscore scoring function retrieved 75% of the native poses in the three highest-ranked solutions for high-quality protein-ligand complexes with default settings. Individual configurations for protein preparation are available, e.g., considering protein ensembles, relevant binding site water molecules, or cofactors. A user-defined number of input conformations for the ligands of interest can be generated fully automated using Conformator. Alternatively, users can also provide externally prepared ligand conformers.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/jamda.htmljamdabiotools:jamdaWeb serviceCommand-line toolhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_0082Structure predictionLinuxWindowsMacOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3816Mol2http://edamontology.org/format_1197InChIhttp://edamontology.org/format_1196SMILEShttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFprotein-ligand docking for small moleculeshttps://proteins.plusServiceA web service to run JAMDA calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneralprotossuses10.1021/acs.jcim.3c01573Primary10.1002/jcc.26522Method10.1021/acs.jcim.0c01095MethodProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderGeoMineGeoMine enables the automated mining of protein-ligand binding sites. Based on individually designed queries, users can search for spatial interaction patterns in huge collections of protein-ligand complexes and binding pockets. The regularly updated GeoMine database relies on the free database systems SQLite and PostgreSQL. It supports radius-based pockets (based on ligands and predicted pockets (based on DoGSite3) for query generation. The query management is based on XML (for the REST service) or JSON in the GUI mode. Its output consists of the query-based superpositions of the matched binding sites and statistics on matching points, distances, and angles.https://www.zbh.uni-hamburg.de/forschung/amd/software/geomine.htmlgeominebiotools:geomineWeb APIWeb servicehttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3336Drug discoveryMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/operation_0306Text mininghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFtextual, numerical, and chemical 3D searches in the PDBhttps://proteins.plusServiceA web service to run GeoMine calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://proteins.plus/help/geomine_restServiceA web API to run GeoMine calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://proteins.plus/help/indexGeneraldogsite3usesprotossuses10.1093/bioinformatics/btaa69332735322Usage10.1021/acs.jcim.6b00561Method10.1021/acs.jmedchem.1c01046Primary10.1007/s10822-024-00563-3UsageProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderStructureProfilerThree-dimensional protein structures play a vital role in drug design. Structure-based design necessitates an in-depth examination of the available quality data before using the structure in computational experiments and for method evaluation. StructureProfiler assists in automatically profiling sets of protein-ligand complex structures based on multiple quality indicators, ranging from model characteristics, e.g., the R factor, and active site features, e.g., bond length deviations, to ligand properties such as electron density support and the validity of torsion angles.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/structureprofiler.htmlStructureProfilerbiotools:StructureProfilerWeb serviceWeb APICommand-line toolhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3572Data quality managementhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_1317Structural biologyLinuxWindowsMacOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_1844Protein geometry validationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFquality profiling for protein-ligand complexeshttps://proteins.plusServiceA web service to run StructureProfiler calculations for protein structures stored in the Protein Data Bank.https://proteins.plus/help/structurechecker_restServiceA web API to run StructureProfiler calculations for protein structures stored in the Protein Data Bank.https://uhh.de/naomiSoftware catalogueLink to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinarieshttps://proteins.plus/help/indexGeneral10.1093/bioinformatics/bty69230124779PrimaryProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderWarPPWarPP predicts the position and orientation of water molecules in small-molecule binding sites. It places and scores water molecules in binding sites of crystallographic structures based on EDIAscorer results and interaction geometries as known from experimentally solved protein structures. WarPP was validated on a high-quality set of 1,500 protein-ligand complexes, containing 20,000 crystallographically observed water molecules. It is sufficiently fast for high-throughput analyses. It correctly places water molecules in approx. 80% of the cases. Users can export the predictions as PDB files for, e.g., molecular docking with JAMDA.https://www.zbh.uni-hamburg.de/forschung/amd/software/warpp.htmlwarppbiotools:warppWeb serviceCommand-line toolWeb APIhttp://edamontology.org/topic_0123Protein propertieshttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3534Protein binding sitesLinuxWindowsMacOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFwater molecule placementhttps://proteins.plusServiceA web service to run WarPP calculations for protein structures stored in the Protein Data Bank.https://proteins.plus/help/warpp_restServiceA web API to run WarPP calculations for protein structures stored in the Protein Data Bank.https://uhh.de/naomiSoftware catalogueLink to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinarieshttps://proteins.plus/help/indexGeneral10.1021/acs.jcim.8b0027130036062PrimaryProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderLifeSoaksLifeSoaks was designed to find solvent channels in macromolecular structures solved by X-ray crystallography. It predicts their accessibility by molecules through an automated annotation of so-called bottleneck radii. It simplifies the process of manually checking a crystal structure for solvent channels. Bottleneck radii can be calculated for solvent channels and small molecule binding sites. The tool is ideally suited for channel analyses before the actual soaking experiments to select the most promising experimental conditions and crystal forms. LifeSoaks runs fully automated and will finish within seconds to minutes for moderately sized crystals.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/lifesoaks.htmllifesoaksbiotools:lifesoaksCommand-line toolWeb servicehttp://edamontology.org/topic_2828X-ray diffractionhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_0091BioinformaticsWindowsMacLinuxOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_2480Structure analysishttp://edamontology.org/operation_0384Accessible surface calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFcalculating bottleneck radii for crystal solvent channelshttps://proteins.plusServiceA web service to run LifeSoaks calculations for protein structures stored in the Protein Data Bank.https://uhh.de/naomi.deSoftware catalogueA link to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneral10.1107/S205979832300582XPrimaryProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderMETALizerMETALizer predicts the coordination geometry of metal ions in metalloproteins. Users can compare potential coordination geometries to those found in the examined structure. The predicted coordination geometries and the observed metal interaction distances can be interactively compared to statistics calculated based on the PDB.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/metalizer.htmlmetalizerbiotools:metalizerWeb APIWeb servicehttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0123Protein propertiesWindowsMacLinuxOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFmetal complex geometry predictionhttps://proteins.plusServiceA web service to run METALizer calculations for protein structures stored in the Protein Data Bank.https://proteins.plus/help/metalizer_restServiceA web API to run METALizer calculations for protein structures stored in the Protein Data Bank.https://proteins.plus/help/indexGeneral10.1093/nar/gkaa235PrimaryProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderEDIAscorerThe electron density score for individual atoms (EDIA) quantifies the electron density fit of each atom in a crystallographically resolved structure. Multiple EDIA values can be combined using the power mean to compute the EDIAm, i.e., the electron density score for a group of several atoms. It enables users to score a set of atoms, such as a ligand, a residue, or an active site.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/ediascorer.htmlediabiotools:ediaCommand-line toolWeb APIWeb servicehttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_2828X-ray diffractionhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_2275Molecular modellingMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFatom-level assessment of the electron density fit for structures solved by X-ray crystallographyhttps://proteins.plusServiceA web service to run EDIAscorer calculations for protein structures stored in the Protein Data Bank.https://proteins.plus/help/edia_restServiceA web API to run EDIAscorer calculations for protein structures stored in the Protein Data Bank.https://uhh.de/naomiSoftware catalogueA link to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinarieshttps://proteins.plus/help/indexGeneralstructureprofilerusedBy10.1021/acs.jcim.7b0039128981269PrimaryProteinsPlus Supportpplus.zbh@uni-hamburg.deSupportNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.deSupportUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956ProviderHyPPIHyPPI classifies a protein-protein complex based on its interaction type into permanent, transient, or crystal artifact. Permanent protein-protein complexes are only stable in their complexed state. Their subunits would denature upon dissociation of the protein-protein complex. Transient protein-protein complexes are stable in the complexed as well as in the monomeric form, depending on the necessary function of the complex. Crystal artifacts have no biological function and are artificially formed during the crystallization process. The discrimination is performed using two characteristics of the protein-protein complex, the hydrophobicity of the interface (ΔGhydrophobic) and the quotient of interface area ratios (IF-quotient). The IF-quotient considers whether the protein-protein interface is symmetric.https://proteins.plus/help/ppippibiotools:ppiWeb APIWeb servicehttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0602Molecular interactions, pathways and networksMacWindowsLinuxOtherde.NBI-biodatade.NBILegacyFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_2949Protein-protein interaction analysishttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBprotein-protein interface classification (permanent, transient, crystal artifact)https://proteins.plusServiceA web service to run HyPPI calculations for protein structures stored in the Protein Data Bank or uploaded structures.https://proteins.plus/help/ppi_restServiceA web API to run HyPPI calculations for protein structures stored in the Protein Data Bank or uploaded structures.https://proteins.plus/help/indexGeneral10.1007/s10822-012-9626-223269578Method10.1093/nar/gkx333PrimaryUsageProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderSIENASIENA is a software pipeline enabling the fully automated construction of protein structure ensembles from the PDB. Starting with a single query structure, all binding sites with high sequence similarity are extracted from the PDB, aligned, and superimposed. SIENA also handles complicated cases, such as comparing binding sites at protein domain interfaces or within multimeric proteins.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/siena.htmlsienabiotools:sienaCommand-line toolWeb APIWeb servicehttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0128Protein interactionsMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_2844Structure clusteringhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFPDB mining and protein binding site ensemble generationhttps://proteins.plusServiceA web service to run SIENA calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.https://proteins.plus/help/siena_restServiceA web API to run SIENA calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.https://uhh.de/naomiSoftware catalogueA link to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneralproteinsplusincludedIn10.1021/acs.jcim.5b0058826759067MethodPrimary10.1021/acs.jcim.5b0021026098831MethodProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderPoseEditPoseEdit automatically generates 2D diagrams of protein-ligand complexes, focusing on the interactions between protein and ligand. Interactions between molecules are estimated by an underlying interaction model that relies on atom types and simple geometric criteria. The structure mining tool GeoMine also uses this model to describe binding sites. In addition, users can manipulate the diagrams by translating, rotating, mirroring parts of the structure, adding additional interactions, or removing them. Furthermore, users can add individual labels or adjust available labels. Users can download the final 2D diagrams for a binding site of interest in JSON or SVG format.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/poseedit.htmlposeeditbiotools:poseeditWeb APIWeb servicehttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3534Protein binding sitesWindowsMacLinuxOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF2D interaction diagram drawing and editinghttps://proteins.plusServiceA web service to run PoseEdit calculations for protein-ligand complexes.https://proteins.plus/help/poseview2_restServiceA web API to run PoseEdit calculations for protein-ligand complexes.https://proteins.plus/help/indexGeneralgeomineusedByprotossuses10.1007/s10822-023-00522-437515714PMC10440272PrimaryProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderPoseViewPoseView automatically generates 2D diagrams of protein-ligand complexes, focusing on the interactions between protein and ligand. Interactions between molecules are estimated by an underlying interaction mode that relies on atom types and simple geometric criteria. It adheres to the conventions of chemical structure diagram generation. The quality of the resulting diagrams is comparable to manually drawn examples from books and scientific publications.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/poseview.htmlposeviewbiotools:poseviewWeb serviceWeb APIhttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3534Protein binding sitesLinuxWindowsMacOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF2D interaction diagram drawinghttps://proteins.plusServiceA web service to run PoseView calculations for protein-ligand complexes.https://proteins.plus/help/poseview_restServiceA web API to run PoseView calculations for protein-ligand complexes.https://proteins.plus/help/indexGeneral10.1021/ml100164p24900245PMC4007829Primary10.1093/bioinformatics/btl15016632493Benchmarking study10.1002/cmdc.20070001017436259Benchmarking study10.1021/ci049958u15154775MethodProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956ProviderProtossProtoss is a fully automated hydrogen atom placement tool for protein-ligand complexes. It adds missing hydrogen atoms to protein structures and detects reasonable protonation states, tautomeric states, and hydrogen coordinates of both protein and ligand molecules by optimizing the hydrogen bond network.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/protoss.htmlprotossbiotools:protossWeb APIWeb servicehttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_0082Structure predictionMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFprediction of protonation states and tautomers and placement of hydrogen atomshttps://proteins.plusServiceA web service to run Protoss calculations.https://proteins.plus/help/protoss_restServiceA web API to run Protoss calculations.https://proteins.plus/help/indexGeneralgeomineusedByjamdausedBy10.1186/1758-2946-6-1224694216PMC4019353Primary10.1186/1758-2946-1-1320298519PMC3225823OtherProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderDoGSite3DoGSite3 was developed for predicting robust and reliable small molecule binding sites and computing their geometrical and chemical descriptors. It is based on the grid-based DoGSite algorithm for predicting pockets and their sub-pockets. The new tool is largely rotation- and translation-invariant due to a normalization procedure before binding site prediction. Known ligands in the structure can be used to bias the grid by sufficiently buried ligand fragments. The output encompasses novel chemical binding site descriptors considering solvent accessibility. Compared to its predecessor, it shows increased robustness through comprehensive parameter optimization. DoGSite3 runs finish within seconds.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/dogsite3.htmldogsite3biotools:dogsite3Command-line toolWeb APIWeb servicehttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0123Protein propertiesMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_3897Ligand-binding site predictionhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFsmall molecule binding site detectionhttps://proteins.plusServiceA web service to run DoGSite3 calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://proteins.plus/help/dogsite3_restServiceA web API to run DoGSite3 calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://uhh.de/naomiSoftware catalogueLink to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneralgeomineusedBy10.1021/acs.jcim.3c0033637130052PrimaryProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderDoGSiteScorerDoGSiteScorer is a grid-based automated pocket detection and analysis tool. It applies a Difference of Gaussian filter to detect potential binding pockets and splits them into sub-pockets. The method solely uses the 3D structure of the protein. Global properties, describing the size, shape, and chemical features of the predicted (sub-)pockets, are calculated. Per default, a simple druggability score based on a linear combination of the three descriptors describing volume, hydrophobicity, and enclosure is provided for each (sub-)pocket. Furthermore, a subset of meaningful descriptors is incorporated in a support vector machine (libsvm) to predict the (sub-)pocket druggability score (values are between zero and one). The higher the score, the more druggable the pocket is estimated to be.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/dogsitescorer.htmldogsitescorerbiotools:dogsitescorerWeb serviceWeb APIhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0123Protein propertiesWindowsMacLinuxOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_3897Ligand-binding site predictionhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFsmall molecule binding site detection and druggability assessmenthttps://proteins.plusServiceA web service to run DoGSiteScorer calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://proteins.plus/help/dogsite_restServiceA web API to run DoGSiteScorer calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database.https://proteins.plus/help/indexGeneral10.1021/ci100241y20945875MethodPrimary10.1093/bioinformatics/bts31022628523MethodProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderCLIFinderCLIFinder is a Galaxy tool designed to identify potential L1 Chimeric Transcripts from RNA-seq data by analyzing paired-end reads in the human genome. It allows customization to detect transcripts initiated by different repeat elements.https://github.com/GReD-Clermont/CLIFinderCLIFinderbiotools:CLIFinder0.5.2ScriptCommand-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3308TranscriptomicsRPerlGPL-3.0Galaxy ToolsGalaxyEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/operation_2403Sequence analysishttps://github.com/GReD-Clermont/CLIFinder/Repositoryhttps://toolshed.g2.bx.psu.edu/repository?repository_id=5c73d1cf20ab37c3Galaxy servicehttps://github.com/GReD-Clermont/CLIFinder/blob/main/README.rstAPI documentationhttps://github.com/GReD-Clermont/CLIFinder/#usageCommand-line options10.1093/bioinformatics/btx67129069308PrimaryAutozygosityMapperAutozygosityMapper is aimed at finding human disease-causing DNA variants in consanguineous families - it builds on HomozgyosityMapper and MutationDistiller. It requires only a (multi-sample) VCF file and the specification of affected and unaffected individuals.https://www.genecascade.org/AutozygosityMapper/autozygositymapperbiotools:autozygositymapperQP-Insights UploaderThis desktop application enables users to upload DICOM data along with associated clinical information to QP-Insights—the data management platform of the UPV Reference Node within EUCAIM.https://drive.eucaim.cancerimage.eu/f/1320qp-insights_uploaderbiotools:qp-insights_uploader1.2.1Desktop applicationhttp://edamontology.org/topic_3384Medical imaginghttp://edamontology.org/topic_3366Data integration and warehousingWindowsMacPythonCC-BY-NC-ND-4.0EUCAIMhttp://edamontology.org/operation_3431Data depositionhttp://edamontology.org/data_3424Raw imagehttp://edamontology.org/format_3548DICOM formathttp://edamontology.org/data_0956Data index reporthttp://edamontology.org/format_3468xlshttp://edamontology.org/format_3580rcchttps://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/qp_insights_uploader/artifacts-tabOtherLink to EUCAIM harborhttps://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/qp_insights_uploader/info-tabDownloads pageLink to EUCAIM Harborhttps://drive.eucaim.cancerimage.eu/f/1320Downloads pageLink to EUCAIM Drivehttps://eucaim.gitbook.io/enduserguide/6-userguide4membersUser manualhttps://www.youtube.com/watch?v=F_nK-V676n8Training materialQuibimhttps://quibim.com/Institutesnp-distsPairwise SNP distance matrix from a FASTA sequence alignmenthttps://github.com/tseemann/snp-distssnp-distsbiotools:snp-distsv1.2.0Command-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0080Sequence analysisCShellGPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0260Sequence alignment conversionhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTATorsten SeemannPersonFabian KlötzlPersonAndrew J PagePersonREGENIEregenie is a C++ program for whole genome regression modelling of large genome-wide association studies.https://rgcgithub.github.io/regenie/regeniebiotools:regeniev4.1http://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3517GWAS studyhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3474Machine learningRFortranShellC++COtherMatureFree of chargeOpen accesshttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3659Regression analysis10.1038/S41588-021-00870-734017140Jonathan Marchinijonathan.marchini@regeneron.comhttps://orcid.org/0000-0003-0610-8322PersonChromBPNetBias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet).https://github.com/kundajelab/chrombpnetchrombpnetbiotools:chrombpnetv1.0.1http://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_0102MappingPythonShellMITMaturehttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_3226Variant prioritisationhttp://edamontology.org/operation_0238Sequence motif discoveryhttps://github.com/kundajelab/chrombpnet/wikiGeneral10.1101/2024.12.25.630221rxdockRxDock is a fast and versatile open-source docking program that can be used
to dock small molecules against proteins and nucleic acids. It is designed for high-throughput virtual screening (HTVS) campaigns and binding mode prediction studies.https://rxdock.gitlab.io/rxdockbiotools:rxdockhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_3336Drug discoveryShellPythonAWKMATLABC++PerlCOtherMaturehttp://edamontology.org/operation_3899Protein-protein docking10.1371/JOURNAL.PCBI.100357124722481PMC3983074Xavier Barrilxbarril@ub.eduPersonGLnexusScalable gVCF merging and joint variant calling for population sequencing projectshttps://github.com/dnanexus-rnd/GLnexusGLnexusbiotools:GLnexusv1.4.1Command-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0605InformaticsPythonC++ShellApache-2.0Maturehttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_3196Genotypinghttps://github.com/dnanexus-rnd/GLnexus/wikiGeneralhttp://dnanexus-rnd.github.io/GLnexusGeneral10.1101/343970NanofiltFiltering and trimming of long read sequencing data.http://nanoplot.bioinf.benanofiltbiotools:nanofiltCommand-line toolhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_3168SequencingPythonGPL-3.0LegacyOpen accesshttp://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_3218Sequencing quality controlhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQhttps://github.com/wdecoster/nanofiltRepository10.1093/BIOINFORMATICS/BTY14929547981PMC6061794Wouter De Costerwouter.decoster@molgen.vib-ua.behttps://orcid.org/0000-0002-5248-8197PersonPepkio Sequence Property CalculatorCalculates sequence-derived molecular properties and related laboratory planning outputs from FASTA and assay setup inputs. The tool supports sequence analysis for DNA, RNA, and protein entries, plus dilution and ligation calculation modes through one API-backed workflow. Programmatic use is available through a Python library and command-line interface that submit run payloads and return structured result objects.https://www.pepkio.com/tools/sequence-property-calculatorpepkio-sequence-property-calculatorbiotools:pepkio-sequence-property-calculator0.1.0Command-line toolLibraryWeb applicationhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3361Laboratory techniqueshttp://edamontology.org/topic_3292BiochemistryPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3434ConversionOne tool endpoint supports three modes (sequence, dilution, ligation) for sequence property analysis and laboratory planning calculations.https://github.com/pepkio/pepkio-sequence-property-calculatorRepositoryhttps://www.pepkio.com/tools/sequence-property-calculatorServicehttps://pypi.org/project/pepkio-sequence-property-calculator/Repositoryhttps://www.pepkio.com/tools/sequence-property-calculatorGeneralhttps://github.com/pepkio/pepkio-sequence-property-calculatorUser manualPepkiohttps://www.pepkio.com/ProjectProviderPepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services.Pepkio Molecular Mass ConverterTranslates spectrophotometer and NanoDrop readings into mass and molar concentrations for dsDNA, ssDNA, ssRNA, and protein from a single anchor input, with optional sequence-specific nearest-neighbor extinction coefficients. A browser calculator supports bidirectional unit conversion, batch processing of up to ninety-six NanoDrop export rows, and A260/A280 purity interpretation with plain-language warnings; a REST API exposes converter, batch, and purity modes for scripted use. Calculator arithmetic is hosted remotely; API clients transmit parameters and return structured result fields and shareable run identifiers.https://www.pepkio.com/tools/mol-mass-converterpepkio-mol-mass-converterbiotools:pepkio-mol-mass-converter0.1.0Command-line toolLibraryWeb applicationhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3361Laboratory techniqueshttp://edamontology.org/topic_3292BiochemistryPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3434ConversionWeb calculator for OD260, mass, and molar conversion across nucleic acids and protein; REST API for converter, batch, and purity modes.https://github.com/pepkio/pepkio-mol-mass-converterRepositoryhttps://www.pepkio.com/tools/mol-mass-converterServicehttps://www.pepkio.com/tools/mol-mass-converterGeneralhttps://github.com/pepkio/pepkio-mol-mass-converterUser manualPepkiohttps://www.pepkio.com/ProjectProviderPepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services.Pepkio RCF RPM Rotor ConverterTranslates between centrifuge RPM and relative centrifugal force using rotor geometry, reporting g-force or speed at rmin, ravg, and rmax. Convert mode handles rpm_to_rcf and rcf_to_rpm with rotor presets or manual radii in mm; transfer mode maps a source RPM on one rotor to an equivalent target RPM at matched rmax RCF; batch mode processes multiple spin steps from CSV or row arrays. A browser calculator and a Python library with command-line interface submit the same parameters to the Pepkio Tools API and return structured results with optional methods text and safety warnings.https://www.pepkio.com/tools/rcf-rpm-rotor-converterpepkio-rcf-rpm-rotor-converterbiotools:pepkio-rcf-rpm-rotor-converter0.1.0Web applicationCommand-line toolLibraryhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3361Laboratory techniquesPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3434ConversionThree modes (convert, transfer, batch) for RPM↔RCF conversion, rotor protocol transfer, and batch CSV processing.https://github.com/pepkio/pepkio-rcf-rpm-rotor-converterRepositoryhttps://www.pepkio.com/tools/rcf-rpm-rotor-converterServicehttps://www.pepkio.com/tools/rcf-rpm-rotor-converterGeneralhttps://github.com/pepkio/pepkio-rcf-rpm-rotor-converterUser manualPepkiohttps://www.pepkio.com/ProjectProviderPepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services.Pepkio Bio Unit ConverterPerforms laboratory unit conversions across molarity, OD600 cell density, C₁V₁ dilution, and related dimensional pairs from mass, volume, molecular weight, and organism-specific OD factors. A browser calculator combines four modes in one tabbed workspace with compound MW lookup, species-aware OD uncertainty ranges, cross-tab chaining, and shareable links; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted use. Calculator arithmetic for the API client is hosted remotely; the client transmits conversion inputs and returns structured results and shareable run identifiers.https://www.pepkio.com/tools/bio-unit-converterpepkio-bio-unit-converterbiotools:pepkio-bio-unit-converter0.1.0Command-line toolLibraryWeb applicationhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3361Laboratory techniqueshttp://edamontology.org/topic_3292BiochemistryPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3434ConversionWeb calculator for molarity, OD600, dilution, and unit conversion in one workspace; Python library and CLI for API-backed automation of the same conversion engine.https://github.com/pepkio/pepkio-bio-unit-converterRepositoryhttps://www.pepkio.com/tools/bio-unit-converterServicehttps://www.pepkio.com/tools/bio-unit-converterGeneralhttps://github.com/pepkio/pepkio-bio-unit-converterUser manualPepkiohttps://www.pepkio.com/ProjectProviderPepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services.Pepkio Mendelian Cross SolverConstructs Punnett squares and offspring genotype and phenotype ratios for complete, incomplete, codominant, ABO multiple-allele, and sex-linked Mendelian crosses from parent genotypes, with step-by-step walkthroughs and reduced ratio output. A browser calculator provides live grids, textbook presets, PNG and SVG export, and shareable links; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted use. Calculator arithmetic for the API client is hosted remotely; the client transmits cross inputs and returns structured grids, ratios, walkthroughs, and shareable run identifiers.https://www.pepkio.com/tools/mendelian-cross-solverpepkio-mendelian-cross-solverbiotools:pepkio-mendelian-cross-solver0.1.0LibraryWeb applicationCommand-line toolhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_0625Genotype and phenotypePythonMITFree of chargeOpen accesshttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_3197Genetic variation analysisWeb calculator for Punnett squares across five inheritance modes; Python library and CLI for API-backed automation of the same Mendelian cross engine.https://github.com/pepkio/pepkio-mendelian-cross-solverRepositoryhttps://www.pepkio.com/tools/mendelian-cross-solverServicehttps://pypi.org/project/pepkio-mendelian-cross-solver/Repositoryhttps://www.pepkio.com/tools/mendelian-cross-solverGeneralhttps://github.com/pepkio/pepkio-mendelian-cross-solverUser manualPepkiohttps://www.pepkio.com/ProjectProviderPepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services.Pepkio HWE Equilibrium StudioEvaluates Hardy-Weinberg equilibrium for diploid loci with two to six alleles using chi-square and Guo-Thompson exact tests, inbreeding coefficient F, and plain-language verdicts from observed genotype counts, allele frequencies, or biallelic disease incidence. A browser calculator provides De Finetti plots, export, and Wright-Fisher simulation under selection, drift, mutation, and migration; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted use. Calculator arithmetic for the API client is hosted remotely; the client transmits genotype or simulation inputs and returns structured results and shareable run identifiers.https://www.pepkio.com/tools/hwe-equilibrium-studiopepkio-hwe-equilibrium-studiobiotools:pepkio-hwe-equilibrium-studio0.1.0Web applicationCommand-line toolLibraryhttp://edamontology.org/topic_3056Population geneticshttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_0625Genotype and phenotypePythonMITFree of chargeOpen accesshttp://edamontology.org/operation_0554Allele frequency distribution analysishttp://edamontology.org/operation_3197Genetic variation analysishttp://edamontology.org/operation_2238Statistical calculationWeb calculator for multiallelic HWE testing and Wright-Fisher simulation; Python library and CLI for API-backed automation of the same population genetics engine.https://github.com/pepkio/pepkio-hwe-equilibrium-studioRepositoryhttps://www.pepkio.com/tools/hwe-equilibrium-studioServicehttps://pypi.org/project/pepkio-hwe-equilibrium-studio/Repositoryhttps://www.pepkio.com/tools/hwe-equilibrium-studioGeneralhttps://github.com/pepkio/pepkio-hwe-equilibrium-studioUser manualPepkiohttps://www.pepkio.com/ProjectProviderPepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services.Pepkio Dose-Response Curve FitterPerforms batch four-parameter and five-parameter logistic regression on multi-compound concentration–response screens to estimate IC50, EC50, pIC50, Hill slope, and related potency metrics with per-compound QC grades. A browser calculator supports CSV upload, curve review, and figure export; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits concentration–response data and returns structured fit results and shareable run identifiers.https://www.pepkio.com/tools/dose-curve-fitterpepkio-dose-curve-fitterbiotools:pepkio-dose-curve-fitter0.1.0Web applicationCommand-line toolLibraryhttp://edamontology.org/topic_0202Pharmacologyhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3361Laboratory techniquesPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3659Regression analysisWeb calculator for HTS dose–response fitting; Python library and CLI for API-backed automation of the same curve-fitting engine.https://github.com/pepkio/pepkio-dose-curve-fitterRepositoryhttps://www.pepkio.com/tools/dose-curve-fitterServicehttps://pypi.org/project/pepkio-dose-curve-fitter/Repositoryhttps://www.pepkio.com/tools/dose-curve-fitterGeneralhttps://github.com/pepkio/pepkio-dose-curve-fitterUser manualPepkiohttps://www.pepkio.com/ProjectProviderPepkio develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services.SeqBenchSeqBench is a free collection of browser-based tools for working with DNA, RNA and protein sequences, including reverse complement, translation, ORF finding, GC content, primer melting temperature, restriction site analysis, codon optimization, pairwise alignment and plasmid visualization. All computation runs client-side in the browser, so input sequences are never uploaded to a server.https://seqbench.comseqbench-onlinebiotools:seqbench-onlineWeb applicationhttp://edamontology.org/topic_0080Sequence analysisFreewareEmergingFree of chargehttp://edamontology.org/operation_0431Restriction site recognitionhttp://edamontology.org/operation_0371DNA translationhttp://edamontology.org/operation_0308PCR primer designhttp://edamontology.org/operation_0236Sequence composition calculationhttp://edamontology.org/operation_0292Sequence alignmentPhylo-MoviesPhylo-Movies is an open-source React and Flask web application, also available as a desktop app, for inspecting ordered phylogenetic tree series. It computes and visualizes subtree-prune-and-regraft transition frames between consecutive trees, helping users see which taxa or subtrees move across sliding-window analyses, bootstrap replicates, and curated tree-series comparisons. The viewer includes timeline playback, tree comparison, MSA context, coloring, analytics, image export, and recording tools.https://enesberksakalli.github.io/phylo-movies/phylo-moviesbiotools:phylo-movies0.98.1Desktop applicationWeb applicationhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0092Data visualisationWindowsMacLinuxPythonJavaScriptTypeScriptMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/operation_0324Phylogenetic tree analysishttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAVisualizes ordered phylogenetic tree series as animated transition movies with comparison, MSA context, movement analytics, image export, and recording support.https://github.com/enesBerkSakalli/phylo-moviesRepositorySource code repository.https://enesberksakalli.github.io/phylo-movies/demo/ServiceStatic browser demo with precomputed example movies.https://github.com/enesBerkSakalli/phylo-movies/issuesIssue trackerhttps://github.com/enesBerkSakalli/phylo-moviesSource codeSource checkout for full web application and backend workflows.0.98.1https://github.com/enesBerkSakalli/phylo-movies/releases/tag/v0.98.1BinariesDesktop convenience builds for macOS, Windows, and Linux.0.98.1https://enesberksakalli.github.io/phylo-movies/manual/User manualResearcher-facing manual.https://github.com/enesBerkSakalli/phylo-movies/blob/main/README.mdGeneralProject overview, installation, usage, citation, and links.https://github.com/enesBerkSakalli/phylo-movies/blob/main/docs/getting-started.mdInstallation instructionsLocal source-checkout setup instructions.https://github.com/enesBerkSakalli/phylo-movies/blob/main/docs/api.mdAPI documentationBackend API documentation.10.64898/2026.04.01.715821PrimarybioRxiv preprint describing the Phylo-Movies method and examples.10.5281/zenodo.20488923Primary0.98.1Archived software release on Zenodo.Enes Berk Sakallienes@lbi-netmed.athttps://github.com/enesBerkSakalliPersonDeveloperPrimary contactCorresponding software contact.Simon E. HaendelerPersonDeveloperArndt von HaeselerPersonDeveloperHeiko A. SchmidtPersonDeveloperLacunaWhen a stroke, tumor, or other focal brain injury damages tissue, understanding its consequences requires placing the lesion within the broader organization of the brain. Lacuna is an open-source toolbox that uses normative reference data from healthy individuals, including connectivity datasets and anatomical atlases, to characterize lesions beyond their anatomical location.
Users provide lesion masks in MNI space, and Lacuna automatically retrieves reference data, performs required processing steps, and generates BIDS-organized outputs. Designed for multicenter research, it standardizes workflows, scales from single cases to large cohorts, supports HPC deployment through containers, and records provenance for reproducible lesion analyses.https://github.com/m-petersen/lacunalacunabiotools:lacunahttp://edamontology.org/topic_3334NeurologyLinuxMacPythonBashOpen accesshttps://lacuna-py.readthedocs.io/en/latest/Command-line optionsnalloNallo is a bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. The pipeline detects a wide range of genetic variants, performs genome assembly,
and reports CpG methylation. It also enables annotation and ranking of variants based on their predicted functional
consequences.https://github.com/genomic-medicine-sweden/nallonallobiotools:nallo0.12.0http://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_3295EpigeneticsGroovyJavaMITFree of chargehttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_0331Variant effect predictionhttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_3226Variant prioritisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_2545FASTQ-like formathttps://github.com/genomic-medicine-sweden/nalloRepositoryhttps://genomic-medicine-sweden.github.io/nallo/latest/User manual10.1093/BIOINFORMATICS/BTAG08641712762PMC12988770Lars Feuklars.feuk@igp.uu.sehttps://orcid.org/0000-0003-2355-2919PersonDeRRDeRR (Detection Dual T-cell receptor in single cell sequencing) is a method for detection of TCR in single cell sequencing data and detection of dual-TCR in scRNA-Seq/scTCR-Seq.https://github.com/GuoBioinfoLab/DeRRderrbiotools:derrScriptCommand-line toolhttp://edamontology.org/topic_3930ImmunogeneticsPythonMatureFree of charge (with restrictions)Open accesshttp://edamontology.org/operation_3359Splittinghttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2572BAMDemultiplex sequence datapython SplitVDJbam.py [OPTIONS]http://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQAIRR compatible V-J gene callingpython DeRR.py [OPTIONS]https://github.com/GuoBioinfoLab/DeRRRepositoryhttps://github.com/GuoBioinfoLab/DeRRSource codehttps://github.com/GuoBioinfoLab/DeRR/blob/main/README.mdQuick start guide10.1093/gpbjnl/qzaf09041051256PrimaryAnyuan Guoguoanyuan@wchscu.cnPersonPrimary contactOBIToolsSet of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.https://git.metabarcoding.org/obitools/obitools/wikis/homeobitoolsbiotools:obitoolsCommand-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_3168SequencingLinuxWindowsMacPythonhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_2403Sequence analysishttp://www.mybiosoftware.com/obitools-scripts-and-library-for-sequence-analysis.htmlSoftware cataloguehttp://metabarcoding.org//obitools/doc/welcome.html#installing-the-obitoolsGeneral10.1111/1755-0998.1242825959493Eric Coissaceric.coissac@inria.frhttp://metabarcoding.org/obitoolsPersonPrimary contactPredictProteinPredictProtein is a protein sequence analysis and structure prediction tool. Users provide a protein sequence, and PredictProtein reports similar sequences, PROSITE sequence motifs, and various types of structure prediction information. You can also use META PredictProtein to submit a sequence to one web form and query several other servers at once, retrieving the results by e-mail.http://ppopen.rostlab.orgpredictproteinbiotools:predictproteinWeb applicationhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0166Protein structural motifs and surfaceshttp://edamontology.org/topic_0078ProteinsLinuxWindowsMachttp://edamontology.org/operation_0468Protein secondary structure prediction (helices)http://edamontology.org/operation_0303Protein fold recognitionhttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://edamontology.org/operation_0474Protein structure predictionhttps://open.predictprotein.org/tutorialsGeneral10.1093/nar/gkg57212824314PMC16897810.1093/nar/gkh37715215403PMC44151510.1093/nar/gkg50812824312PMC168915PredictProtein Supporthelp@predictprotein.orgPersonPrimary contactSNAPThe Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.https://korflab.ucdavis.edu/software.htmlsnapbiotools:snapCommand-line toolhttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_3053GeneticsLinuxChttp://edamontology.org/operation_2454Gene predictionhttps://www.mybiosoftware.com/snap-20130216-gene-prediction-tool.htmlSoftware cataloguehttps://korflab.ucdavis.edu/software.htmlGeneral10.1186/1471-2105-5-5915144565PMC421630ifkorf@ucdavis.eduhttps://korflab.ucdavis.edu/PersonPrimary contactFlavoTyperFlavoTyper is a bioinformatics tool that performs in silico serotyping of Flavobacterium psychrophilum genome assemblies.https://forge.inrae.fr/eric.duchaud/flavotyperflavotyperbiotools:flavotyperCommand-line toolWeb servicehttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_3397Veterinary medicineMacLinuxPythonApache-2.0EmergingOpen accesshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/data_0925Sequence assemblyhttp://edamontology.org/format_1929FASTAhttps://flavotyper-125bcf.pages-forge.inrae.fr/User manualRnaChipIntegratorUtility that performs integrated analyses of 'gene' data (a set of genes or other genomic features) with 'peak' data (a set of regions, for example ChIP peaks) to identify the genes nearest to each peak, and vice versa.https://github.com/fls-bioinformatics-core/RnaChipIntegratorrnachipintegratorbiotools:rnachipintegrator3.0.0Command-line toolhttp://edamontology.org/topic_3307Computational biologyPythonArtistic-2.0MatureFree of chargehttp://edamontology.org/operation_2424Comparisonhttp://edamontology.org/data_1255Sequence featureshttp://edamontology.org/format_3475TSVRnaChipIntegrator GENES PEAKSpyBigWigA python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.https://github.com/deeptools/pyBigWigpybigwigbiotools:pybigwig0.3.25Libraryhttp://edamontology.org/topic_3307Computational biologyCMITMaturehttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_2945Data analysishttp://edamontology.org/data_1255Sequence featureshttp://edamontology.org/format_3006bigWighttp://edamontology.org/format_3004bigBedMONAI LabelMONAI Label is an intelligent open source image labeling and learning tool that enables users to create annotated datasets and build AI annotation models for clinical evaluation. MONAI Label enables application developers to build labeling apps in a serverless way, where custom labeling apps are exposed as a service through the MONAI Label Server.https://monai.readthedocs.io/projects/label/en/latest/monai_labelbiotools:monai_label0.8.5Web applicationhttp://edamontology.org/topic_3303MedicineLinuxWindowsPythonApache-2.0MatureFree of chargehttp://edamontology.org/operation_3553Image annotation10.1007/978-3-031-17027-0_2DeepConsensusDeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.https://github.com/google/deepconsensusdeepconsensusbiotools:deepconsensus1.2.0Command-line toolhttp://edamontology.org/topic_3307Computational biologyLinuxPythonBSD-3-ClauseMatureFree of chargehttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_0850Sequence setdeepconsensus run --subreads_to_ccs=shard_id.subreads_to_ccs.bam --ccs_bam=shard_id.ccs.bam --checkpoint=model/checkpoint --output=shard_id.output.fastq10.1038/s41587-022-01435-736050551DAZZ_DBA database system designed to store, organize, and manage large-scale nucleotide sequencing read data (like PacBio reads) for the Dazzler genome assemblerhttps://github.com/thegenemyers/DAZZ_DBdazz_dbbiotools:dazz_db1.0Command-line toolhttp://edamontology.org/topic_3307Computational biologyLinuxCOtherLegacyFree of chargehttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/data_2887Nucleic acid sequence record1. fasta2DB [-v] <path:db> ( -f<file> | -i[<name>] | <input:fasta> ... )Cookiecutter BioinformaticsA cookiecutter template for bioinformatics projects, with a focus on building bioinformatics workflows that can run on the MPI-IE cluster according to FAIR principles.https://github.com/maxplanck-ie/cookiecutter-bioinformatics-projectcookiecutter_bioinformaticsbiotools:cookiecutter_bioinformaticsCommand-line toolhttp://edamontology.org/topic_0091BioinformaticsPythonMITEmergingFree of chargehttp://edamontology.org/operation_3762Service compositionhttp://edamontology.org/data_1049Directory namePepkio Knowledge Explorer: Single-Cell Long-Read RNA SequencingA static web application presents an interactive knowledge graph of single-cell long-read RNA sequencing literature synthesized from seven source papers. Users navigate mind-tree, network graph, guided learning-path, and Sankey views linking platforms, protocols, methods, and software. A benchmark tab provides 34 question-answer pairs with category and difficulty filters, exportable as JSON or CSV for LLM and agent evaluation.https://github.com/pepkio/kg-single-cell-long-read-rna-sequencingpepkio-kg-single-cell-long-read-rna-sequencingbiotools:pepkio-kg-single-cell-long-read-rna-sequencing0.1.0Web applicationhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_4028Single-cell sequencingJavaScriptMITFree of chargeOpen accesshttp://edamontology.org/operation_0306Text mininghttp://edamontology.org/operation_0337VisualisationInteractive exploration of synthesized literature knowledge plus a downloadable benchmark Q&A subset for LLM evaluation.https://github.com/pepkio/kg-single-cell-long-read-rna-sequencingRepositoryhttps://www.pepkio.com/blogs/articles/single-cell-long-read-rna-sequencingOtherEditorial synthesis article for the knowledge explorer topic.https://www.pepkio.com/blogs/articles/single-cell-long-read-rna-sequencingGeneralhttps://github.com/pepkio/kg-single-cell-long-read-rna-sequencingUser manualPepkiohttps://www.pepkio.com/ProjectProviderPepkio (https://www.pepkio.com/) develops software tools, curated research knowledge resources, and bioinformatics analysis services for life science researchers.SigmaCVAuto-generates clean, customizable academic CVs from open research data (OpenAlex, ORCID, Crossref, DataCite, Open Editors Plus). A single canonical CV object drives every output format (HTML, PDF, DOCX, LaTeX, Markdown); citations render through CSL; and the account holder is matched by persistent identifier (ORCID / OpenAlex ID) rather than name string. Free for individuals, open-source, and FAIR by design.https://sigmacv.orgsigmacvbiotools:sigmacv0.1.0Web applicationMacWindowsLinuxJavaScriptTypeScriptApache-2.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0335Data formattinghttp://edamontology.org/operation_0226Annotationhttps://github.com/BasileChretien/sigmacvRepositoryhttps://github.com/BasileChretien/sigmacv/issuesIssue trackerhttps://github.com/BasileChretien/sigmacvSource codehttps://github.com/BasileChretien/sigmacv#readmeGeneral10.5281/zenodo.20594123Other0.1.0Basile Chrétienchretien.basile.jean.bernard.u4@s.mail.nagoya-u.ac.jphttps://orcid.org/0000-0002-7483-2489DeveloperMaintainerPrimary contactPDB-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 IDhttps://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 support