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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BioWorks Resource Report Resource Website 500+ mentions |
BioWorks (RRID:SCR_014594) | software resource, data processing software, software application, data analysis software | A a configurable software package for peptide and protein mass spectrometry analyses. It includes the SEQUEST search algorithm to identify separate proteins in complex mixtures, interactive navigation tools to filter and sort protein summaries, customized spectral plots, and chromatograms using the PEPMATCH and PEPMAP tools. This software also has batch processing capabilities to improve throughput by queuing up several files, and custom-build proprietary databases, index databases, and retrieve databases through a public server. | mass spectrometry, mass spectrometry analysis, sequest, algorithm, navigation, protein, chromatogram, pepmatch, pepmap, proprietary database, index, retrieve, FASEB list | has parent organization: Thermo Fisher Scientific | Commercial | SCR_014594 | 2026-08-05 10:46:10 | 897 | ||||||||||
|
FATCAT Resource Report Resource Website 100+ mentions |
FATCAT (RRID:SCR_014631) | software resource, web application | Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | web server, protein, comparison, structure, flexible protein structure, protein structure comparison, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: FATCAT Flexible Structural Neighborhood |
NIGMS GM101457; NIGMS GM63208; NIGMS GM076221; NSF DBI-0349600 |
PMID:14534198 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fatcat | https://bio.tools/fatcat | SCR_014631 | (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists, (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT) | 2026-08-05 10:46:11 | 139 | |||||
|
GROMACS Resource Report Resource Website 5000+ mentions |
GROMACS (RRID:SCR_014565) | software toolkit, software application, simulation software, software resource | Software package created to perform molecular dynamics. Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Can also be used for research on non-biological systems, such as polymers. | simulation, molecular dynamics, software package, software toolkit, biochemical, molecule, protein, lipid, nucleic acid, bond interaction, bio.tools |
is used by: CHARMM-GUI is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
European Research Council ; Swedish eScience Research Center ; Stream Computing Performance Engineers ; Nvidia ; Swedish Research Council ; Swedish Foundation for Strategic Research ; Swedish National Infrastructure for Computing ; Swedish Foundation for International Cooperation in Research and Higher Education |
PMID:26620784 DOI:10.1016/0010-4655(95)00042-E |
Free, Available for download | biotools:gromacs, OMICS_05081 | https://bio.tools/gromacs, https://sources.debian.org/src/gromacs/, https://github.com/gromacs/gromacs | SCR_014565 | Gromacs | 2026-08-05 10:46:11 | 8264 | |||||
|
Bioclipse Resource Report Resource Website 10+ mentions |
Bioclipse (RRID:SCR_014914) | software resource, data processing software, software application, data analysis software | Open source downloadable application which contains a framework for managing and analyzing chemical compounds, as well as supports editing in 2D, processing large collections of molecules in tables, calculate various types of properties, and more cheminformatics functionality. This software also is used for the management and analysis of biological sequences (DNA, RNA, and protein), and relates the chemical structures and a target and then describes them using mathematical descriptors and models them using statistical methods. Bioclipse is equipped with a scripting language (Bioclipse Scripting Language or BSL) which can be used to automate tasks or create reusable snippets that can be shared with others, | framework, chemical, compound, 2d, molecule, cheminformatic, biological, dna, rna, protein, mathematical | Commercial | SCR_014914 | 2026-08-05 10:46:13 | 17 | |||||||||||
|
iDTI-ESBoost Resource Report Resource Website |
iDTI-ESBoost (RRID:SCR_016720) | iDTI-ESBoost | software application, simulation software, service resource, software resource | Software tool for identification of Drug Target Interaction using Evolutionary and Structural features with Boosting. Used to predict drug-protein interactions. | identification, drug, target, interaction, evolutionary, structural, feature, boost, predict, protein | PMID:29255285 | Free, Freely available | http://farshidrayhan.pythonanywhere.com/iDTI-ESBoost/ | SCR_016720 | identification of Drug Target Interaction using Evolutionary and Structural features with Boosting | 2026-08-05 10:46:44 | 0 | |||||||
|
Entrez Resource Report Resource Website 10+ mentions |
Entrez (RRID:SCR_016640) | data or information resource, portal, data access protocol, software resource, web service | Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ. | global, query, cross, database, search, retrival, system, database, nucleotide, protein, sequence, data, genomic, mapping, structure, reference |
is affiliated with: PubChem BioAssay is related to: National Library of Medicine has parent organization: NCBI works with: Batch Entrez works with: Biotite |
Free, Freely available | SCR_016640 | 2026-08-05 10:46:37 | 15 | ||||||||||
|
OmicsNet Resource Report Resource Website 10+ mentions |
OmicsNet (RRID:SCR_016724) | web service, data access protocol, software resource, production service resource, service resource, analysis service resource | Web based tool to create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space (genes/proteins, microRNAs, transcription factors or metabolites). | create, molecular, interaction, network, visually, 3D, gene, protein, microRNA, transcription factor, metabolite, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Natural Sciences and Engineering Research Council of Canada ; Genome Canada ; Canada Research Chairs Program |
PMID:29878180 | Free, Freely available | biotools:omicsnet | https://bio.tools/omicsnet | SCR_016724 | 2026-08-05 10:46:38 | 39 | ||||||
|
Clonotator Resource Report Resource Website |
Clonotator (RRID:SCR_016730) | data processing software, data access protocol, software application, image analysis software, alignment software, data analysis software, sequence analysis software, software resource, web service | Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data. | screening, annotation, cDNA, sequence, amino acid, align, reference, database, protein, disease, mutation, transcriptomic, data | has parent organization: University of California at San Francisco; California; USA | Free, Freely available, Registration required | https://willseylab.com/clonotator/ | SCR_016730 | 2026-08-05 10:46:44 | 0 | |||||||||
|
PMI-Byonic Resource Report Resource Website 10+ mentions |
PMI-Byonic (RRID:SCR_016735) | Byonic | software resource, data processing software, software application, data analysis software | Software package for advanced peptide and protein identification by tandem mass spectrometry. Allows to define unlimited number of variable modification type and allows the user to set a separate limit on the number of occurrences of each modification type. | Byonic, Protein Metrics Inc., peptide, protein, identification, mass, spectrometry | NIGMS R21 GM085718 | PMID:23255153 | Commercially available | SCR_016735 | Protein Metrics Inc. Byonic, PMI-Byonic, PMI Byonic, Byonic | 2026-08-05 10:46:38 | 22 | |||||||
|
Metascape Resource Report Resource Website 1000+ mentions |
Metascape (RRID:SCR_016620) | web service, data access protocol, software resource, data analysis service, production service resource, service resource, analysis service resource | Web service to analyze gene or protein lists. Provides automated meta analysis tools to understand pathways within a group of orthogonal target-discovery studies. | analyze, gene, protein, list, data, annotate, resource, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Freely available | biotools:Metascape | https://bio.tools/Metascape | SCR_016620 | 2026-08-05 10:46:42 | 3483 | ||||||||
|
Biostrings Resource Report Resource Website 100+ mentions |
Biostrings (RRID:SCR_016949) | data processing software, software application, sequence analysis software, data analysis software, software resource | Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. | manipulation, biological, string, memory, efficient, container, sequence, set, DNA, RNA, protein |
is used by: riboWaltz is listed by: Bioconductor is related to: R Project for Statistical Computing has parent organization: Stanford University; Stanford; California |
Free, Available for download, Freely available | https://web.stanford.edu/class/bios221/labs/biostrings/lab_1_biostrings.html | SCR_016949 | 2026-08-05 10:46:46 | 167 | |||||||||
|
OmicsSIMLA Resource Report Resource Website 1+ mentions |
OmicsSIMLA (RRID:SCR_017011) | software toolkit, software application, simulation software, software resource | Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version. | multi, omics, data, simulator, disease, genomic, epigenomic, transcriptomic, proteomic, genome, sequencing, protein, RNA | is listed by: OMICtools | Ministry of Science and Technology in Taiwan | DOI:10.1101/426510 | Freely available, Available to download, Free | OMICS_31363 | SCR_017011 | 2026-08-05 10:46:47 | 1 | |||||||
|
ProSight Lite Resource Report Resource Website 10+ mentions |
ProSight Lite (RRID:SCR_016908) | software resource, data processing software, software application, data analysis software | Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data. | matching, single, protein, sequence, proteomics, top-down proteomics, mass, spectrometric, data, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Northwestern University; Illinois; USA is provided by: National Resource for Translational and Developmental Proteomics |
NIGMS R01 GM067193; NIDA P30 DA018310 |
DOI:10.1002/pmic.201400313 | Free, Available for download, Freely available | biotools:prosigh_lite | https://bio.tools/prosight_lite | SCR_016908 | 2026-08-05 10:46:46 | 14 | ||||||
|
National Resource for Translational and Developmental Proteomics Resource Report Resource Website |
National Resource for Translational and Developmental Proteomics (RRID:SCR_016907) | NRTDP | data or information resource, portal, training resource, organization portal, service resource | Organization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists. | protein, mass, spectrometry, proteomics, measurement, targeted, untargeted, analysis |
has parent organization: Northwestern University; Illinois; USA provides: ProSight Lite |
NIGMS P41 GM108569 | SCR_016907 | The National Resource for Translational and Developmental Proteomics, NRTDP | 2026-08-05 10:46:40 | 0 | ||||||||
|
Clustal 2 Resource Report Resource Website 1000+ mentions |
Clustal 2 (RRID:SCR_017055) | data processing software, image analysis software, software application, data visualization software, alignment software, software resource | Software tool for nucleotide sequence alignment. Graphical version of multiple sequence alignment program for DNA and proteins. Windows interface for ClustalW multiple sequence alignment program. Provides integrated environment for performing multiple sequence and profile alignments and analyzing results. Available on Linux, Mac and Windows. | graphical, multiple, sequence, alignment, DNA, protein |
is related to: Clustal W2 is related to: Clustal Omega |
Science Foundation Ireland ; INSERM ; CNRS ; Ministère de la Recherche et Technologie ; EMBL |
PMID:17846036 PMID:9396791 |
Free, Available for download, Freely available | biotools:clustal2 | http://www.clustal.org/download/clustalx_help.html, https://bio.tools/clustal2 | SCR_017055 | Clustalx, CLUSTAL_X, clustalx, clustal X, clustal2 | 2026-08-05 10:46:49 | 1480 | |||||
|
CPTAC Resource Report Resource Website 100+ mentions |
CPTAC (RRID:SCR_017135) | data or information resource, portal, consortium, disease-related portal, topical portal, organization portal | Clinical proteomic tumor analysis consortium to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, in order to understand molecular basis of cancer that is not possible through genomics and to accelerate translation of molecular findings into clinic. Operates through Proteome Characterization Centers, Proteogenomic Translational Research Centers, and Proteogenomic Data Analysis Centers. CPTAC investigators collaborate, share data and expertise across consortium, and participate in consortium activities like developing standardized workflows for reproducible studies. | identify, protein, alteration, cancer, genome, clinical, study, proteome, proteogenomic, tumor, data, analysis, consortium, reproducibility | has parent organization: National Cancer Institute | cancer | SCR_017135 | Clinical Proteomic Tumor Analysis Consortium | 2026-08-05 10:46:43 | 131 | |||||||||
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University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility Resource Report Resource Website |
University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility (RRID:SCR_017192) | CTR Bioinformatics Core Facility | core facility, training service resource, access service resource, data analysis service, production service resource, service resource, analysis service resource | Core provides assistance with experimental design, RNA sequencing, whole genome and targeted sequencing, methylation sequencing, protein alignment, microscopy image analysis, and training. | bioinformatics, sequencing, RNA, genome, methylation, protein, alignment, data, image, analysis | has parent organization: University of Cambridge; Cambridge; United Kingdom | Restricted | SCR_017192 | Center for Trophoblast Research, Centre for Trophoblast Research, Bioinformatics Core Facility, University of Cambridge | 2026-08-05 10:46:44 | 0 | ||||||||
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PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | web service, data access protocol, software resource, data analysis service, production service resource, service resource, analysis service resource | Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. | Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
NIGMS R01 GM071966; NHGRI HG005998; NIGMS P50 GM071508 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-08-05 10:46:53 | 7 | ||||||||
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GeneMarkS-T Resource Report Resource Website 100+ mentions |
GeneMarkS-T (RRID:SCR_017648) | software resource, data processing software, software application, data analysis software | Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark. | Identification, protein, coding, region, RNA, transcript, gene, discovery, eukaryotic, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Georgia Institute of Technology; Georgia; USA |
NHGRI HG000783 | PMID:25870408 | Restricted | biotools:GeneMarkS-t | https://bio.tools/GeneMarkS-T | SCR_017648 | 2026-08-05 10:46:55 | 113 | ||||||
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GO Gene Ontology Consortium and Knowledgebase Resource Report Resource Website 1+ mentions |
GO Gene Ontology Consortium and Knowledgebase (RRID:SCR_017505) | GOC | data or information resource, portal, consortium, organization portal | Consortium integrates resources from variety of research groups, from model organisms to protein databases to biological research communities actively involved in development and implementation of Gene Ontology. Mission to develop up to date, comprehensive, computational model of biological systems, from molecular level to larger pathways, cellular and organism level systems. | Integrate, resource, model, organism, protein, database, gene, ontology, develope, cellular, system | NHGRI HG002273; NHGRI U24 HG012212 |
SCR_017505 | GO Consortium, Gene Ontology Consortium | 2026-08-05 10:46:48 | 8 |
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