plantiSMASHPlantiSMASH is a specialized extension of antiSMASH for the identification and analysis of biosynthetic gene clusters (BGCs) in plant genomes. It supports advanced plant-specific detection rules and features for comparative genomics, visualization, and more.https://plantismash.bioinformatics.nl/plantismashbiotools:plantismash2.0-beta4http://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_0085Functional genomicsMacWindowsLinuxAGPL-3.0https://github.com/plantismash/plantismash/releasesSoftware package2.0-beta4https://plantismash.github.io/documentation/General10.1093/nar/gkx305PMC55701731.010.1016/j.jmb.2026.16979841962628Primary2.0plantiSMASH 2.0: Improvements to Detection, Annotation, and Prioritization of Plant Biosynthetic Gene ClustersDigestedProteinDBDigestedProteinDB provides a scalable computational infrastructure for indexing and querying peptide cleavage data. Designed for seamless integration into high-throughput mass spectrometry pipelines, it enables low-latency searches and advanced filtering of digested protein datasets to accelerate experimental spectra cross-referencing.https://digestedproteindb.pbf.hrdigestedproteindbbiotools:digestedproteindbDatabase portalhttp://edamontology.org/topic_0121ProteomicsOpen Neuroscience GraphThe Open Neuroscience Graph (openneuroscience.org) is an open-access, curated knowledge graph that maps the open science ecosystem in neuroscience as a browsable digital garden. Built from an Obsidian vault and published as a static website using Quartz, the project replaces traditional linear presentation with a networked structure of interlinked Markdown notes. Bidirectional links, full-text search, and an integrated graph visualization allow users to navigate thematic relationships dynamically rather than sequentially. The complete source material is openly available to sustain, replicate and extend the resource, includding all Markdown content, media attachments, Quartz configuration files, and site customizations. Researchers, educators, and open-science practitioners may explore the site directly, download the vault for offline use in Obsidian, or fork the material to build new, derivative knowledge bases.
PID=https://doi.org/10.5281/zenodo.20181900https://openneuroscience.orgopen_neuroscience_graphbiotools:open_neuroscience_graph1.0.0doi:10.5281/zenodo.20181900doi1.0.0Database portalhttp://edamontology.org/topic_4019BiosciencesWindowsiOSAndroidLinuxMacJavaScriptCC-BY-4.0EmergingFree of chargeOpen accessTrainingFrancehttps://gitlab.com/icm-institute/dac/opensciencegraphRepositoryhttps://gitlab.com/icm-institute/dac/opensciencegraphSource code1.0.0https://gitlab.com/icm-institute/dac/opensciencegraph/-/blob/main/CONTRIBUTING.md?ref_type=headsContributions policy10.5281/zenodo.20181900Primary1.0.0Stephen Whitmarshstephen.whitmarsh@icm-institute.orghttps://stephenwhitmarsh.comhttps://orcid.org/0000-0002-3969-6565phantasusIt is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.http://bioconductor.org/packages/release/bioc/html/phantasus.htmlphantasusbiotools:phantasus1.0.2Libraryhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3518Microarray experimenthttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_3308TranscriptomicsLinuxMacWindowsRMITBioConductorFree of chargehttp://edamontology.org/operation_3432Clusteringhttp://edamontology.org/operation_3223Differential gene expression analysishttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_0337Visualisationhttps://alserglab.wustl.edu/phantasusMirrorhttps://github.com/alserglab/phantasus/issuesIssue trackerhttps://github.com/alserglab/phantasus/issuesRepositoryhttp://bioconductor.org/packages/release/bioc/src/contrib/phantasus_1.0.2.tar.gzSoftware packagehttp://bioconductor.org/packages/release/bioc/manuals/phantasus/man/phantasus.pdfUser manualAlexey Sergushichevalsergbox@gmail.comPersonPrimary contactfgseaThe package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.http://bioconductor.org/packages/release/bioc/html/fgsea.htmlfgseabiotools:fgsea1.12.0RRID:SCR_020938rridLibraryCommand-line toolhttp://edamontology.org/topic_3053GeneticsMacLinuxWindowsRMITBioConductorhttp://edamontology.org/operation_2436Gene-set enrichment analysishttps://github.com/alserglab/fgsea/Repositoryhttp://bioconductor/packages/release/bioc/src/contrib/fgsea_1.0.2.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/fgsea.htmlUser manual10.1101/060012PrimaryAlexey Sergushichevalsergbox@gmail.comPersonPrimary contactTenDNA DNA Format ConverterTool for converting raw DNA data files between 23andMe, AncestryDNA, MyHeritage, and FamilyTreeDNA formats.https://tendna.com/en/dna-convertertendna_dna_format_converterbiotools:tendna_dna_format_converterdoi:10.5281/zenodo.20185958doi1.0.0Web servicehttp://edamontology.org/topic_0091BioinformaticsWindowsPHPMITFile ExchangeMatureFree of chargeOpen accesshttps://github.com/milaza/dna-raw-data-converter-23andme-myheritage-ancestry/RepositoryOpen-source documentation and source code for the TenDNA DNA Format Converter, including raw DNA format guides, compatibility notes, and conversion examples for 23andMe, AncestryDNA, MyHeritage, and FamilyTreeDNA.https://tendna.com/en/dna-converterServiceThe tool supports DNA file format compatibility, raw genotype data restructuring, and cross-platform conversion for genealogy and personal genomics workflows.
Features include:
- raw DNA format conversion
- compatibility between major consumer DNA services
- support for TSV and CSV genotype files
- online processing without manual editinghttps://github.com/milaza/dna-raw-data-converter-23andme-myheritage-ancestry/OtherGitHub repository with source code and documentation for raw DNA format conversion between major consumer genomics platforms.10.5281/zenodo.201859581.0.0https://doi.org/10.5281/zenodo.20185958Metastasis risk prediction in Lung cancerΑ radiomics-based machine learning model, for the prediction of the occurrence of metastasis within two years of the initial lung cancer diagnosis combining information from the tumor and the peritumoral area as well clinical information of the patient.https://www.med.auth.gr/en/content/laboratory-computing-medical-informatics-and-biomedical-imaging-technologiesmetastasis_risk_prediction_in_lung_cancerbiotools:metastasis_risk_prediction_in_lung_cancer1.0Command-line toolPythonRCC-BY-NC-ND-4.0EUCAIMMatureFree of chargeRestricted access10.1016/j.cmpb.2025.109029PrimaryIoanna Chouvardaioannach@auth.grhttps://scholar.google.com/citations?user=QgcrIzEAAAAJ&hl=el&oi=srahttps://orcid.org/0000-0001-8915-6658PersonPrimary contactProfessor, Aristotle University of ThessalonikiProstate ISUP classificationThis software implements a AI pipeline for the detection of clinically significant prostate cancer (csPCa) from multiparametric MRI images combined with routine clinical data. The specific tasks performed by the software include: radiomics extraction from whole-gland prostate gland and sub-regions based on T2-weighted and DWI from MRI sequences; data harmonization at both image and feature levels to correct for vendor and acquisition batch effects; and classification using machine learning models to stratify patients according to the likelihood of clinically significant prostate cancer. The inference model is available.https://www.med.auth.gr/en/content/laboratory-computing-medical-informatics-and-biomedical-imaging-technologiesprostate_isup_classificationbiotools:prostate_isup_classification1.0Command-line toolPythonRCC-BY-NC-ND-4.0EUCAIMMatureFree of chargeRestricted access10.1109/ISBI56570.2024.10635588Ioanna Chouvardaioannach@auth.grhttps://scholar.google.com/citations?user=QgcrIzEAAAAJ&hl=el&oi=srahttps://orcid.org/0000-0001-8915-6658PersonPrimary contactProfessor, Aristotle University of ThessalonikiSAPPHIRESecure & Privacy-preserving Prototype-based Heterogenous-fl Integrated with Random-number Embeddinghttps://cancerimage.eu/sapphire-SecureFLbiotools:sapphire-SecureFLScripthttp://edamontology.org/topic_4045Cybersecurityhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_4044Data protectionhttp://edamontology.org/topic_3384Medical imagingLinuxWindowsPythonEUCAIMEmerginghttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_2426Modelling and simulationhttps://drive.eucaim.cancerimage.eu/s/Z3pbpGCc5opwZkn?dir=/&editing=false&openfile=trueOtherImage Quality Assessment metrics (IQA) for XNAT platformDocker images developped at the Euro-BioImaging MED-Hub and National Research Council (CNR) for the XNAT platform hosted by University of Turin. A suite of four Image Quality Assessment (IQA) metrics designed to evaluate the perceptual quality of preclinical and clinical image datasets within the XNAT platform at the scan and subject levels. The tool outputs Excel files containing the mean and median for each metric and scan, as well as PNG files with corresponding histogram plots.https://github.com/FerielRamdhane/Image-Quality-Assessment-metrics-IQA-for-XNAT-platformimage_quality_assessment_metrics_iqa_for_xnat_platformbiotools:image_quality_assessment_metrics_iqa_for_xnat_platform1.0ScriptCommand-line toolhttp://edamontology.org/topic_3572Data quality managementMacLinuxWindowsPythonMATLABCC-BY-NC-ND-4.0EUCAIMFree of chargeOpen accesshttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/iqaxnat_scan/info-tabRepositoryhttps://drive.eucaim.cancerimage.eu/s/Q7x86RTMiZJdq97GeneralFeriel Romdhaneferielromdhane@yahoo.frhttps://orcid.org/0000-0002-5854-9341Euro-BioImaging ERICpreclinicaldata@eurobioimaging.euhttps://www.eurobioimaging.eu/National Research Councilhttps://www.ibb.cnr.it/NLmCED FilterThe NLmCED (Non Local mean Coherence Enhancing Diffusion) filter is a denoising tool aimed to reduce Rician Noise in 3D MR images. It is a combination between two filters such as the Non-Local mean filter and the Anisotropic Diffusion tensor method with an estimator of Rician noise. The NLmCED filter can benefit from the noise reduction capabilities of the NLM filter while maintaining the edge-preserving characteristics of anisotropic diffusion.https://github.com/FerielRamdhane/NLmCED-Filter/tree/mainnlmced_filterbiotools:nlmced_filter1.0Scripthttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_3444MRIhttp://edamontology.org/topic_3384Medical imagingMacLinuxWindowsPythonMATLABCC-BY-NC-ND-4.0EUCAIMFree of chargeOpen accesshttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3548DICOM formathttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nlmced/info-tabRepositoryGithub Linkhttps://drive.eucaim.cancerimage.eu/s/L5iwmo6WknyLoWwGeneral10.1504/IJCVR.2018.09001210.1002/mrm.28676Feriel Romdhaneferielromdhane@yahoo.frhttps://orcid.org/0000-0002-5854-9341ExomeFlowExomeFlow is a Python package that provides a complete, automated Whole Exome Sequencing (WES) analysis workflow from raw FASTQ files to functionally annotated variants in a single reproducible CLI command.
It aims to be the standard high-level pipeline for WES analysis in Python, combining GATK best-practice variant calling, hard filtering, and ANNOVAR annotation into one modular, maintainable package. It handles cohort-level processing (multiple samples), checkpointing for resumable runs, structured logging, and parallel execution out of the box.https://pypi.org/project/exomeflow/exomeflowbiotools:exomeflow1.0.91.0.8WorkflowCommand-line toolhttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_2533DNA mutationLinuxPythonBashFreewareEmergingFree of chargeOpen accesshttps://pypi.org/project/exomeflow/Repositoryhttps://pypi.org/project/exomeflow/Software package1.0.08https://pypi.org/project/exomeflow/Generalfastpusesbio-samtoolsincludesgatk_haplotype_callerincludesRobin Kumaritsrobintomar@gmail.comhttps://pypi.org/project/exomeflow/https://orcid.org/0009-0002-9084-2019PersonDeveloperFrameXploreFrameXplore is a Google Colab notebook that extends ColabFold to automatically identify and correct disulfide bonds in cysteine‑rich protein structures. After a standard ColabFold prediction, it extracts all cysteine residues, computes Cα–Cα and S–S distances, identifies true disulfide bonds using geometric cutoffs (Cα–Cα < 6.5 Å, S–S < 2.5 Å), writes a corrected PDB with proper CONECT records, and provides an interactive 3D view.https://github.com/Vidhusv/FRAMEXPLORERframexplorebiotools:framexplore1.0.0doi:10.5281/zenodo.20135079doiWeb applicationhttp://edamontology.org/topic_4019BiosciencesLinuxMacWindowsPythonMITEmergingFree of chargeOpen accesshttps://github.com/Vidhusv/FRAMEXPLORERRepositoryGitHub repository with source code, documentation, and logohttps://github.com/Vidhusv/FRAMEXPLORER/issuesIssue trackerReport bugs, suggest features, or ask questionshttps://github.com/Vidhusv/FRAMEXPLORER/archive/refs/heads/main.zipSource codeLatest version of the complete repository as a ZIP file1.0.0https://raw.githubusercontent.com/Vidhusv/FRAMEXPLORER/main/FrameXplore.ipynbBinariesDirect download of the Colab notebook (.ipynb file). Can be run locally or uploaded to Google Colab.1.0.0https://github.com/Vidhusv/FRAMEXPLORER/blob/main/README.mdGeneralQuick start guide, example test case, methodology explanation, citation, and repository contents10.1038/s41592-022-01488-135637307PMC9184281PrimaryColabFold: making protein folding accessible to all. Nature Methods, 2022.Vidhu S Vijayvidhuvijay2003@gmail.comhttps://github.com/Vidhusvhttps://orcid.org/0009-0009-1182-2089PersonDeveloperMaintainerMS Bioinformatics student at Amrita Vishwa Vidyapeetham; creator and maintainer of FrameXplore.METALizerMETALizer 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 serviceWeb APIhttp://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 propertiesMacLinuxWindowsOtherde.NBI-biodatade.NBIMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_2480Structure analysishttp://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_3814SDFhttp://edamontology.org/format_1476PDBhttps://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 Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderCycSimLong-read sequencing data contain context-dependent errors, where certain bases are more likely to be misread depending on their surrounding sequence. Most existing simulators introduce errors randomly, which overlooks these error biases and only approximates the overall error rate. CycSim takes a different approach by modeling errors in a k-mer–dependent manner, enabling more realistic and biologically accurate error simulation.
CycSim is easy to train and supports all types of long-read sequencing data. It currently provides pre-trained models for BGI CycloneSEQ, PacBio HiFi, and Oxford Nanopore Q20 data. Users can also quickly train their own custom models using a BAM file of reads aligned to a reference genome.https://github.com/BioEarthDigital/CycSimcycsimbiotools:cycsimBIGR xnattoolsxnattools is a python package with a set of modules for performing various operations on data stored in XNAT servers. The main purpose is to provide one standardized platform for running operations on XNAT servers. The package currently contains four tools that use this platform: dicom to nifty conversion, thumbnail generation from dicom, DICOM header data collection, in bulk downloading of a project.https://gitlab.com/radiology/radiomics/xnattoolsbigr_xnattoolsbiotools:bigr_xnattoolsv0.0.1LibraryLinuxMacWindowsPythonApache-2.0EUCAIMEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3096Data editinghttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_3436Aggregationhttps://gitlab.com/radiology/radiomics/xnattoolsSource codev0.0.1xnatpyusesxnatusesMartijn PA Starmansm.starmans@erasmusmc.nlhttps://bigr.nl/member/martijn/https://orcid.org/0000-0001-5086-7153PersonPrimary contactErasmus MCInstituteProviderTSENATTSENAT is a R package for quantifying and modeling isoform-usage complexity across RNA-seq samples using Tsallis entropy, a scale-dependent information-theoretic measure of transcript heterogeneity.https://github.com/gallardoalba/TSENATtsenatbiotools:tsenat0.99.0Command-line toolhttp://edamontology.org/topic_3308TranscriptomicsMacLinuxWindowsRGPL-3.0-or-laterTranscriptomicsEmergingFree of chargehttp://edamontology.org/operation_3680RNA-Seq analysishttp://edamontology.org/data_2603Expression dataresult <- TSENAT(analysis)https://bioconda.github.io/recipes/r-tsenat/README.htmlSoftware packagehttps://gallardoalba.github.io/TSENAT/User manualGlyComboCLIGlyComboCLI is an open source command line interface for combinatorial glycan composition determination to identify glycans in MS acquisitions of glycan-containing samples in text or mzML formats. This application enables rapid extraction of precursor m/z values from mzML files, a vendor-neutral format that ensures cross-platform compatibility.https://github.com/Protea-Glycosciences/GlyComboCLIglycomboclibiotools:glycombocli0.1.0Command-line toolhttp://edamontology.org/topic_3292Biochemistryhttp://edamontology.org/topic_3391OmicsLinuxWindowsC#Apache-2.0EmergingFree of chargeOpen accessToolsSystems Biologyhttp://edamontology.org/operation_3214Spectral analysishttp://edamontology.org/operation_0236Sequence composition calculationhttp://edamontology.org/data_0943Mass spectrumhttp://edamontology.org/format_3244mzMLRequires MS2 scans with precursor m/z annotated if using the mzml approachGlyComboCLI.exe -F=".\masses.txt" -D=Native -R=Reduced -T=Da -E=0.6 -A=Neutral -hMax=9 -nMin=2 -nMax=10https://github.com/Protea-Glycosciences/GlyComboCLITechnical monitoringMonitored GitHub repositoryhttps://github.com/Protea-Glycosciences/GlyComboCLI/releases/latestDownloads pagehttps://hub.docker.com/r/proteaglycosciences/glycombocliContainer filehttps://glycombocli.readthedocs.io/en/latest/Quick start guidemsconvertusesChristopher Ashwoodchris@proteaglyco.comhttps://orcid.org/0000-0001-5944-6179PersonPrimary contactMaia Kellyhttps://orcid.org/0000-0002-9383-1107PersonDeveloperFLIRTFLIRT is a Feature generation tooLkIt for weaRable daTa such as that from your smartwatch or smart ring. With FLIRT you can easily transform wearable data into meaningful features which can then be used for example in machine learning or AI models.https://github.com/im-ethz/flirtflirtbiotools:flirtLibraryhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_3300Physiologyhttp://edamontology.org/topic_3572Data quality managementMacLinuxWindowsPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_3937Feature extractionhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_3108Experimental measurementhttp://edamontology.org/format_3752CSVhttps://flirt.readthedocs.io/en/latest/User manualGeneral10.1016/J.CMPB.2021.10646134736174Simon FöllMartin MaritschFederica SpinolaVarun MishraparadigmaParadigma is a toolbox for processing and feature extraction from wearable sensor data to identify digital biomarkers specifically tailored for Parkinson’s disease.https://github.com/biomarkersParkinson/paradigmaparadigmabiotools:paradigma1.1.1WorkflowSuitehttp://edamontology.org/topic_3360Biomarkershttp://edamontology.org/topic_3334NeurologyLinuxPythonApache-2.0EmergingFree of chargehttp://edamontology.org/operation_1812Data parsinghttp://edamontology.org/operation_2990Classificationhttp://edamontology.org/operation_3937Feature extractionhttp://edamontology.org/data_3275Phenotype namehttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_3108Experimental measurementhttp://edamontology.org/format_2333Binary formathttp://edamontology.org/format_3464JSONhttps://research-software-directory.org/software/paradigmaSoftware cataloguehttps://github.com/biomarkersParkinson/paradigma/issuesIssue trackerhttps://pypi.org/p/paradigmaSoftware cataloguehttps://biomarkersparkinson.github.io/paradigma/Training materialUser manual10.5281/zenodo.13838392PreprintDICHROWEBA server that supports several different algorithms for the analysis of Circular Dichroism (CD) spectra for the prediction of protein secondary structure. Results also contain a graphical comparison of calculated versus experimental results.http://dichroweb.cryst.bbk.ac.uk/html/home.shtmldichrowebbiotools:dichrowebRRID:SCR_018125rridWeb applicationhttp://edamontology.org/topic_3542Protein secondary structurehttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0078ProteinsLinuxWindowsMachttp://edamontology.org/operation_2488Protein secondary structure comparisonhttp://edamontology.org/operation_0319Protein secondary structure assignmenthttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://edamontology.org/operation_2416Protein secondary structure analysishttp://dichroweb.cryst.bbk.ac.uk/html/userguide_dichroweb.shtmlGeneral10.1093/nar/gkh37115215473PMC44150910.1093/bioinformatics/18.1.21111836237Contact Formhttp://dichroweb.cryst.bbk.ac.uk/html/bugreport.shtmlPersonPrimary contactRatioPathPython library for large-scale processing, analysis, and transformation of whole-slide pathology images (WSIs)https://rationai.github.io/ratiopath/ratiopathbiotools:ratiopath1.4.0Libraryhttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_3474Machine learningMacLinuxWindowsMITEUCAIMFree of chargeOpen accessRepeatAfterMeRepeatAfterMe is a package for the extension of repetitive DNA cores. The tool automatically extends a multiple sequence alignment that may represent only a fragment of a longer repetitive sequence family.https://github.com/Dfam-consortium/RepeatAfterMerepeataftermebiotools:repeataftermev0.0.7Command-line toolhttp://edamontology.org/topic_0622GenomicsMacLinuxCCC0-1.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_30092bithttp://edamontology.org/data_1017Sequence rangehttp://edamontology.org/format_3585bed6./RAMExtend -ranges test/extension-test2.tsv -twobit test/extension-test2.2bitRobert HubleyPersonDeveloperLightLogRProcess Data from Wearable Light Loggers and Optical Radiation Dosimeters.
Import, processing, validation, and visualization of personal light exposure measurement data from wearable devices. The package for R statistical software implements features such as the import of data and metadata files, conversion of common file formats, validation of light logging data, verification of crucial metadata, calculation of common parameters, and semi-automated analysis and visualization.https://tscnlab.github.io/LightLogR/lightlogrbiotools:lightlogr0.10.3Libraryhttp://edamontology.org/topic_4010Open sciencehttp://edamontology.org/topic_4019Bioscienceshttp://edamontology.org/topic_3379Preclinical and clinical studiesMacLinuxWindowsRMITMatureFree of chargeOpen accesshttps://github.com/tscnlab/LightLogRRepositoryhttps://lists.lrz.de/mailman/listinfo/lightlogr-usersMailing listhttps://github.com/tscnlab/LightLogR/issuesIssue trackerhttps://cran.r-project.org/package=LightLogRSoftware packagein an R environment run:
install.packages("LightLogR")0.11.3https://tscnlab.github.io/LightLogR/Generalhttps://tscnlab.github.io/LightLogR_webinar/Training material10.21105/joss.0760140123959PMC7617517Johannes Zaunerjohannes.zauner@tum.dehttps://orcid.org/0000-0003-2171-4566PersonMaintainerGenErodeWorkflow for whole genome sequencing analysis, including patterns of genome erosion. Written in Snakemake workflow language.https://github.com/NBISweden/GenErodegenerodebiotools:generodeWorkflowhttp://edamontology.org/topic_0622GenomicsOtherGPL-3.0Maturehttp://edamontology.org/operation_0368Sequence maskinghttp://edamontology.org/operation_3211Genome indexinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/operation_3218Sequencing quality controlhttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2572BAMhttps://github.com/NBISweden/GenErodeGeneralhttps://github.com/NBISweden/GenErode/wikiUser manual10.1186/s12859-022-04757-035698034PMC9195343MethodTransVarGenetic element and variation annotator for transcripts that is able to operate on multiple sequence coordinates, including genomic, cDNA, and protein.https://github.com/zwdzwd/transvartransvarbiotools:transvarCommand-line toolhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_0622GenomicsPythonMIThttp://edamontology.org/operation_0361Sequence annotationhttps://github.com/zwdzwd/transvar/blob/master/README.mdGeneralhttps://transvar.readthedocs.io/en/latest/User manual10.1038/nmeth.362226513549PMC4772859MethodEUCAIM-MR BPE quantificationThe following tool computes background parenchyma enhancement quantification on DCE-MRI at baseline and first time point with enhancement.https://github.com/philips-internal/eucaimeucaim-mr_bpe_quantificationbiotools:eucaim-mr_bpe_quantificationCommand-line toolhttp://edamontology.org/topic_3474Machine learningWindowsLinuxPythoneucaimEUCAIMRestricted accessToxinPred3ToxinPred3.0 - A webserver to predict toxic and non-toxic peptide.https://webs.iiitd.edu.in/raghava/toxinpred3/toxinpred3biotools:toxinpred3https://webs.iiitd.edu.in/raghava/toxinpred3/Service10.1016/j.compbiomed.2024.10892639038391Dr. Gajendra P. S. Raghavaraghava@iiitd.ac.inhttps://webs.iiitd.edu.in/raghava/SIENASIENA 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 serviceWeb APIhttp://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 interactionsWindowsLinuxMacOtherde.NBI-biodatade.NBIMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_2844Structure clusteringhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0244Protein flexibility and motion analysishttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0295Structure 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 accessionstatisticshttps://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 Supportproteinsplus.zbh@lists.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 APIWeb servicehttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3534Protein binding sitesWindowsLinuxMacOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_2844Structure clusteringhttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_1777Protein function predictionhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_3898Metal-binding site predictionhttp://edamontology.org/operation_0306Text mininghttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_0321Protein model validationhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_2575Protein binding site predictionhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_2949Protein interaction analysishttp://edamontology.org/operation_0244Protein flexibility and motion analysishttp://edamontology.org/operation_2949Protein-protein interaction analysishttp://edamontology.org/operation_0249Protein geometry calculationhttp://edamontology.org/operation_0360Structural similarity searchhttp://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_3814SDFhttp://edamontology.org/format_1196SMILEShttps://proteins.plusServicehttps://proteins.plus/help/indexGeneraldogsitescorerincludesdogsite3includesediaincludessienaincludesmetalizerincludesstructureprofilerincludesjamdaincludesgeomineincludesmicrominerincludesposeeditincludesposeviewincludesprotossincludeslifesoaksincludesppiincludes10.1093/nar/gkx33328472372PMC5570178Primary10.1093/nar/gkaa23532297936PMC7319454Usage10.1093/nar/gkac30535489057PMC9252762Usage10.1093/nar/gkaf37740326518PMC12230695UsageProteinsPlus Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderMicroMinerMicroMiner 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_0091BioinformaticsWindowsLinuxMacOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://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 accessionhttps://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.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service Issuessoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderfastahackfastahack is a library for indexing and extracting sequences and subsequences from FASTA files. The library provides a FASTA reader and indexer that can be embedded into applications which would benefit from directly reading subsequences from FASTA files. The library automatically handles index file generation and use.https://github.com/ekg/fastahackfastahackbiotools:fastahack1.0Libraryhttp://edamontology.org/topic_0080Sequence analysisWindowsLinuxMacC++MITMatureFree of chargeOpen accesshttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttps://github.com/ekg/fastahackRepositoryhttps://github.com/ekg/fastahack/blob/master/READMEGeneralErik Garrisonerik.garrison@bc.eduStructureProfilerThree-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:StructureProfilerCommand-line toolWeb serviceWeb APIhttp://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 biologyWindowsLinuxMacOtherde.NBI-biodatade.NBIMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/operation_0249Protein geometry calculationhttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttps://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 Supportproteinsplus.zbh@lists.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 Bioinformatics00g30e956InstituteProviderHyPPIHyPPI 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 networksWindowsLinuxMacOtherde.NBIde.NBI-biodataLegacyFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_2949Protein-protein interaction analysishttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBProbability score for interface classificationhttps://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 Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service 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 APIWeb servicehttp://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 propertiesWindowsLinuxMacOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_1777Protein function predictionhttp://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_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionComputational detection of protein binding pockets Protein binding pockets Property statistics of all protein binding pocketshttps://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 Supportproteinsplus.zbh@lists.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 serviceWeb APIhttp://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 propertiesWindowsLinuxMacOtherde.NBI-biodatade.NBIMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_1777Protein function predictionhttp://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_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttps://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 Supportproteinsplus.zbh@lists.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 discoveryWindowsLinuxMacOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0306Text mininghttp://edamontology.org/operation_2421Database searchhttp://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 accessionhttps://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 Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service 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:warppCommand-line toolWeb APIWeb servicehttp://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 sitesWindowsLinuxMacOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttps://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 Supportproteinsplus.zbh@lists.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 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:jamdaCommand-line toolWeb servicehttp://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 predictionWindowsLinuxMacOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_0482Protein-ligand dockinghttp://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_3814SDFhttp://edamontology.org/format_1196SMILEShttps://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 Supportproteinsplus.zbh@lists.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 Bioinformatics00g30e956InstituteProviderProtossProtoss 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 serviceWeb APIhttp://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 predictionWindowsLinuxMacOtherde.NBI-biodatade.NBIMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_2949Protein interaction 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 accessionhttps://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 Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service 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 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 sitesWindowsLinuxMacOtherde.NBI-biodatade.NBIMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttps://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 Supportproteinsplus.zbh@lists.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 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 sitesWindowsLinuxMacOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttps://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 Supportproteinsplus.zbh@lists.uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956ProviderEDIAscorerThe 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 serviceWeb APIhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_2828X-ray diffractionhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_2275Molecular modellingWindowsLinuxMacOtherde.NBI-biodatade.NBIMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_0321Protein model validationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFScore for structure quality assessment on a global or atomistic levelhttps://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 Supportproteinsplus.zbh@lists.uni-hamburg.deSupportNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.deSupportUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956ProviderLifeSoaksLifeSoaks 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_0091BioinformaticsWindowsLinuxMacOtherde.NBIde.NBI-biodataMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttps://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 Supportproteinsplus.zbh@lists.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 Bioinformatics00g30e956InstituteProviderGSC (Genotype Sparse Compression)Genotype Sparse Compression (GSC) is an advanced tool for lossless compression of VCF files, designed to efficiently store and manage VCF files in a compressed format. It accepts VCF/BCF files as input and utilizes advanced compression techniques to significantly reduce storage requirements while ensuring fast query capabilities. In our study, we successfully compressed the VCF files from the 1000 Genomes Project (1000Gpip3), consisting of 2504 samples and 80 million variants, from an uncompressed VCF file of 803.70GB to approximately 1GB.https://github.com/luo-xiaolong/GSCgsc_genotype_sparse_compressionbiotools:gsc_genotype_sparse_compression1.1HifiasmHifiasm: a haplotype-resolved assembler for accurate Hifi readshttps://github.com/chhylp123/hifiasmhifiasmbiotools:hifiasm0.16.1Command-line toolhttp://edamontology.org/topic_0196Sequence assemblyCC++MIThttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_0524De-novo assemblyhttps://hifiasm.readthedocs.io/en/latest/General10.1038/s41592-020-01056-533526886PMC7961889CB-Dock2CB-Dock2 is an improved version of the CB-Dock server for protein-ligand blind docking, integrating cavity detection, docking and homologous template fitting.https://cadd.labshare.cn/cb-dock2/cb-dock2biotools:cb-dock2Web applicationhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0209Medicinal chemistryMacLinuxWindowsNot licensedFree of chargehttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/operation_2575Binding site predictionhttp://edamontology.org/operation_3899Protein-protein dockinghttp://edamontology.org/operation_4009Small molecule designhttps://cadd.labshare.cn/cb-dock2/php/manual.phpUser manual10.1093/nar/gkac39435609983PMC9252749Yang Caocao@scu.edu.cnhttps://orcid.org/0000-0002-1925-2123PersonYang Liuhttps://orcid.org/0000-0002-2517-9436EvolViewWeb server for displaying, managing and customizing phylogenetic trees.http://www.evolgenius.info/evolview.htmlevolviewbiotools:evolview2Web applicationhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_0621Model organismsLinuxWindowsMachttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/operation_0558Phylogenetic tree annotationhttp://edamontology.org/operation_0326Phylogenetic tree editinghttp://edamontology.org/operation_0324Phylogenetic tree analysishttp://edamontology.org/operation_3478Phylogenetic tree reconstructionhttps://github.com/evolgeniusteam/EvolviewDocumentationGeneral10.1093/nar/gks57622695796PMC339430710.1093/nar/gkw37027131786PMC4987921Evolview Teamevolgenius.team@gmail.comPersonPrimary contactClipKIT in the browserClipKIT in the browser provides a web-based application for fast online trimming of multiple sequence alignments, enhancing accessibility for phylogenetics research. It uses cloud-based resources to efficiently trim alignments while retaining phylogenetically informative sites.https://clipkit.genomelybio.comclipkitbiotools:clipkithttp://edamontology.org/topic_0194Phylogenomicshttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_3192Sequence trimminghttps://clipkit.genomelybio.com/#/termsTerms of usehttps://clipkit.genomelybio.com/#/helpUser manual10.1093/NAR/GKAF32540260744PMC12230650Jacob L Steenwykjlsteenwyk@berkeley.eduhttps://orcid.org/0000-0002-8436-595XPersonslow5-doradoFork of dorado (high-performance, easy-to-use, open source analysis engine for Oxford Nanopore reads) that support S/BLOW5https://github.com/hiruna72/slow5-doradoslow5-doradobiotools:slow5-dorado1.1.1Command-line toolhttp://edamontology.org/topic_4056Long-read sequencinghttp://edamontology.org/topic_0080Sequence analysisLinuxC++Otherhttp://edamontology.org/operation_3185Base-callinghttp://edamontology.org/data_0924Sequence trace