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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Yeast Resource Center Resource Report Resource Website 1+ mentions |
Yeast Resource Center (RRID:SCR_007942) | YRC | biomedical technology research center, training resource | Biomedical technology research center that (1) exploits the budding yeast Saccharomyces cerevisiae to develop novel technologies for investigating and characterizing protein function and protein structure (2) facilitates research and extension of new technologies through collaboration, and (3) actively disseminates data and technology to the research community. Through collaboration, the YRC freely provides resources and expertise in six core technology areas: Protein Tandem Mass Spectrometry, Protein Sequence-Function Relationships, Quantitative Phenotyping, Protein Structure Prediction and Design, Fluorescence Microscopy, Computational Biology. | systems biology technology center, protein function, protein structure, mass spectrometry, protein, structure prediction, fluorescence microscopy, computational biology, sequence, function, phenotyping | has parent organization: University of Washington; Seattle; USA | NCRR ; NIGMS P41 GM103533 |
nif-0000-03650 | SCR_007942 | YRC | 2026-09-19 12:58:39 | 6 | |||||||
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NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis Resource Report Resource Website 1+ mentions |
NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis (RRID:SCR_009009) | Mass Spectrometry Resource, WU Mass Spectrometry Resource | biomedical technology research center, training resource | Biomedical technology research center that develops mass spectrometry-based tools for the study of proteins, lipids and metaboilites. These include biomarker identification, stable isotope mass spectrometry and the analysis of intact proteins. Our goals are: * to conduct basic research in the science of mass spectrometry * to establish collaborative research projects with scientists at WU and at other institutions * to provide a service in mass spectrometry * to educate and train students in mass spectrometry * to disseminate results of our research and descriptions of the subject of mass spectrometry | systems biology technology center, mass spectrometry, protein, lipid, metaboilite, biomarker, isotope, analysis | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIGMS ; NCRR 2P41RR00954 |
nlx_152688 | SCR_009009 | Mass Spectrometry Resource at Washington University in St. Louis, Washington University Mass Spectrometry Resource | 2026-09-19 12:58:41 | 1 | |||||||
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Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center Resource Report Resource Website |
Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center (RRID:SCR_009668) | BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center | access service resource, core facility, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core provides services: RT PCR service, Gene expression profiling service, Proteomics analysis service, Bioinformatics and Systems Biology analyses, Next Generation Sequencing Service, Affymetrix Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates. Core proteomics facility for the Dana-Farber/Harvard Cancer Center. Workflows and algorithms for analysis of next-generation sequencing data including RNA-Seq, ChIP-Seq, Epigenetics-Seq and DNA seq, Comprehensive workflow for analysis of Microbiome sequencing data, Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data. Pipelines: MALDI Tissue imaging and targeted quantitative proteomics. | RT PCR, transcriptome, epigenome, metabolomics, profiling, assay, protein, expression, pathway, data, bioinformatics, analysis, next, generation, sequencing, human, mouse, array, tissue, imaging |
is listed by: Eagle I is related to: Beth Israel Deaconess Medical Center Labs and Facilities is related to: Harvard University Labs and Facilities has parent organization: Harvard University; Cambridge; Massachusetts |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156126 | http://www.bidmcgenomics.org/ | SCR_009668 | Beth Israel Deaconess Medical Center, BIDMC | 2026-09-19 12:58:42 | 0 | ||||||
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Protein Prospector Resource Report Resource Website 500+ mentions |
Protein Prospector (RRID:SCR_014558) | software resource, software toolkit | A package of over twenty mass spectrometry-based tools primarily geared toward proteomic data analysis and database mining. It can be run from the command line, but is primarily used through a web browser, and there is a public website that allows anyone to use the software without local installation. Tandem mass spectrometry analysis tools are used for database searching and identification of peptides, including post-translationally modified peptides and cross-linked peptides. Support for isotope and label-free quantification from this type of data is provided. MS-Viewer software allows sharing and displaying of annotated spectra from many different tandem mass spectrometry data analysis packages. Other tools include software for analyzing peptide mass fingerprinting data (MS-Fit); prediction of theoretical fragmentation of peptides (MS-Product); theoretical chemical or enzymatic digestion of proteins (MS-Digest); and theoretical modeling of the isotope distribution of any chemical, including peptides (MS-Isotope). Searches using amino acid sequence can be used to identify homologous peptides in a database (MS-Pattern); the use of the combination of amino acid sequence and masses can be used for homologous peptide and protein identification using MS-Homology. Tandem mass spectrometry peak list files can be filtered for the presence of certain peaks or neutral losses using MS-Filter. Given a list of proteins, MS-Bridge can report all potential cross-linked peptide combinations of a specified mass. Given a precursor peptide mass and information about known amino acid presence, absence, or modifications, MS-Comp can report all amino acid combinations that could lead to the observed mass. | database search program, database search, database management, peptide, protein, mass spectrometry, ms, utility program, batch msms, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of California at San Francisco; California; USA |
Open source, Freely available to academic researchers | biotools:proteinprospector | https://bio.tools/proteinprospector | SCR_014558 | ProteinProspector | 2026-09-19 12:58:12 | 595 | |||||||
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GPS Resource Report Resource Website 50+ mentions |
GPS (RRID:SCR_016374) | GPS | algorithm resource, software resource | Software that detects kinase-specific phosphorylation sites. GPS provides a platform able to perform its prediction based on a group-based phosphorylation scoring algorithm. It allows users to query multiple protein sequences through a batch prediction mode. | phosphorylate, protein, seq, predictive, substrate, site, kinase, mass spectrometry | PMID:18463090 | Free for academic use, Request for commercial use, Available for download | SCR_016374 | Group-based Prediction System, GPS: Group-based Prediction System, Group-based Prediction System (GPS) | 2026-09-19 12:58:15 | 69 | ||||||||
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kbDNA Inc. Resource Report Resource Website |
kbDNA Inc. (RRID:SCR_016570) | biomaterial supply resource, material resource | Commercial provider of antibodies, antigens and recombinant proteins from Braintree, Massachusetts . Biotechnology company which provides custom oligonucleotides synthesis service. | commercial, biotechnology, company, antibody, antigen, recombinant, protein, custom, synthesis, oligonucleotide | SCR_016570 | 2026-09-19 12:58:15 | 0 | ||||||||||||
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RefSeq Resource Report Resource Website 10000+ mentions |
RefSeq (RRID:SCR_003496) | data or information resource, database | Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases. | reference sequence, transcript, protein, dna, rna, plasmid, organelle, virus, genome, nucleic acid, ortholog, paralog, haplotype, nucleotide sequence, gene expression, blast, gold standard, bio.tools |
is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: BeetleBase is related to: EcoGene is related to: INSDC is related to: HFV Database is related to: RefSeqGene is related to: NCBI Protein Database is related to: RefSeqGene is related to: UniParc at the EBI is related to: NCBI Nucleotide is related to: UniParc is related to: ProRepeat is related to: NCBI Virus is related to: Codon and Codon-Pair Usage Tables is related to: RefSeq non-redundant proteins has parent organization: NCBI |
PMID:24316578 PMID:24259432 PMID:22121212 PMID:18927115 PMID:17130148 PMID:15608248 |
Free, Available for download, Freely available | SCR_016579, nif-0000-03397, OMICS_01659, biotools:refseq, r3d100011306 | ftp://ftp.ncbi.nlm.nih.gov/refseq, https://bio.tools/refseq, https://doi.org/10.17616/R3HP70 | SCR_003496 | RefSeq, , Reference Sequence Database, Reference Sequence, Reference Sequences, NCBI | 2026-09-19 12:56:40 | 19506 | ||||||
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PRINTS Resource Report Resource Website 100+ mentions |
PRINTS (RRID:SCR_003412) | PRINTS | data or information resource, database | Compendium of protein fingerprints. Diagnostic fingerprint database. | compedium, protein, fingerprint, diagnostic, database, FASEB list | has parent organization: University of Manchester; Manchester; United Kingdom | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03338 | http://130.88.97.239/PRINTS/index.php | SCR_003412 | 2026-09-19 12:56:40 | 427 | |||||||
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NCBI Taxonomy Resource Report Resource Website 100+ mentions |
NCBI Taxonomy (RRID:SCR_003256) | NCBI Taxonomy | data or information resource, database | Database for a curated classification and nomenclature that contains the names of all organisms that are represented in the public sequence databases with at least one nucleotide or protein sequence. Data provided encompasses archaea, bacteria, eukaryota, viroids and viruses. The NCBI taxonomy database is not a primary source for taxonomic or phylogenetic information. Furthermore, the database does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts. Consequently, the NCBI taxonomy database is not a phylogenetic or taxonomic authority and should not be cited as such. | viroid, virus, nucleotide, protein, sequence, phylogeny, taxonomic, taxonomy, nomenclature, cladistics, classification, animal, genetic code, gold standard |
is used by: NIF Data Federation is used by: Vertebrate Taxonomy Ontology is listed by: re3data.org is related to: Taxonomy is related to: NEWT is related to: Phenoscape Knowledgebase is related to: EBIMed is related to: GOTaxExplorer is related to: Whatizit is related to: Integrated Manually Extracted Annotation has parent organization: NCBI is parent organization of: NCBITaxon |
PMID:18940862 PMID:18940867 |
Free, Freely available | nif-0000-03179, r3d100010776 | http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html, https://doi.org/10.17616/R3X039 | SCR_003256 | NCBI Taxonomy Browser, Taxonomy Browser, Entrez Taxonomy Browser, NCBI Taxonomy Database | 2026-09-19 12:56:39 | 296 | |||||
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ProNIT Resource Report Resource Website 10+ mentions |
ProNIT (RRID:SCR_003431) | ProNIT | data or information resource, database | Database that provides experimentally determined thermodynamic interaction data between proteins and nucleic acids. It contains the properties of the interacting protein and nucleic acid, bibliographic information and several thermodynamic parameters such as the binding constants, changes in free energy, enthalpy and heat capacity. | interaction, protein, nucleic acid, protein-nucleic acid interaction, thermodynamic, binding constant, free energy, enthalpy, heat capacity | is listed by: OMICtools | Japan Society for the Promotion of Science ; Advanced Technology Institute Inc. |
PMID:16381846 PMID:11987161 PMID:11724731 |
Free, Freely available | nif-0000-03347, OMICS_00541 | http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html, http://www.rtc.riken.go.jp/jouhou/pronit/pronit.html | SCR_003431 | 2026-09-19 12:56:40 | 12 | |||||
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Biomine Resource Report Resource Website 1+ mentions |
Biomine (RRID:SCR_003552) | Biomine | data or information resource, database, service resource | Service that integrates cross-references from several biological databases into a graph model with multiple types of edges, such as protein interactions, gene-disease associations and gene ontology annotations. Edges are weighted based on their type, reliability, and informativeness. In particular, it formulates protein interaction prediction and disease gene prioritization tasks as instances of link prediction. The predictions are based on a proximity measure computed on the integrated graph. | gene, protein, genetics, visualization, connection, biological entity, protein interaction, disease gene, link prediction |
is related to: Entrez Gene is related to: Gene Ontology is related to: HomoloGene is related to: InterPro is related to: OMIM is related to: STRING is related to: UniProtKB is related to: UniProt is related to: GoMapMan has parent organization: University of Helsinki; Helsinki; Finland |
PMID:22672646 | nlx_157687 | SCR_003552 | 2026-09-19 12:56:40 | 4 | ||||||||
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Jenalib: Jena Library of Biological Macromolecules Resource Report Resource Website 1+ mentions |
Jenalib: Jena Library of Biological Macromolecules (RRID:SCR_003031) | JenaLib | data or information resource, database | Database aimed at disseminating information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, basic information on the architecture of biopolymer structures is available. The JenaLib intends to fulfill both scientific and educational needs. Authors who are willing to make available images or coordinates to the scientific community via the Image Library of Biological Macromolecules are requested to contact the author. A PDB/SWISS-PROT cross-reference database combines information from both PDB and SWISS-PROT, thus providing significantly more cross-references than either PDB or SWISS-PROT. The existing brief descriptions of X-ray, NMR and FTIR methods for structure determination are supplemented by information on circular dichroism. | protein, nucleic acid, macromolecule, image, structure, rna, dan, carbohydrate, amino acid, nucleotide |
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Nucleic Acid Database has parent organization: Fritz Lipmann Institute; Jena; Germany |
BMBF | PMID:11752308 PMID:10592237 PMID:8872391 |
Free, Freely available | nif-0000-03062 | https://jenalib.leibniz-fli.de/ | SCR_003031 | IMB Jena Image Library of Biological Macromolecules, Image library of biological macromolecules, Jena Library of Biological Macromolecules | 2026-09-19 12:56:38 | 1 | ||||
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Proteome Analyst Specialized Subcellular Localization Server Resource Report Resource Website 1+ mentions |
Proteome Analyst Specialized Subcellular Localization Server (RRID:SCR_003143) | PA-SUB | analysis service resource, data analysis service, production service resource, service resource | Web server specialized to predict the subcellular localization of proteins using established machine learning techniques. | subcellular localization, protein, machine learning, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Alberta; Alberta; Canada |
PMID:14990451 | Free, Available for download, Freely available | biotools:pa-sub, OMICS_01631 | https://psort.org/#:~:text=Proteome%20Analyst's%20Subcellular%20Localization%20Server, proteins%20to%20many%20localization%20sites. | SCR_003143 | 2026-09-19 12:56:39 | 1 | ||||||
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ASAP: the Alternative Splicing Annotation Project Resource Report Resource Website 10+ mentions |
ASAP: the Alternative Splicing Annotation Project (RRID:SCR_003415) | ASAP | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. Database to access and mine alternative splicing information coming from genomics and proteomics based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence. ASAP provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing. They developed an automated method for discovering human tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs), which involves classifying human EST libraries according to tissue categories and Bayesian statistical analysis. They use the UniGene clusters of human Expressed Sequence Tags (ESTs) to identify splices. The UniGene EST's are clustered so that a single cluster roughly corresponds to a gene (or at least a part of a gene). A single EST represents a portion of a processed (already spliced) mRNA. A given cluster contains many ESTs, each representing an outcome of a series of splicing events. The ESTs in UniGene contain the different mRNA isoforms transcribed from an alternatively spliced gene. They are not predicting alternative splicing, but locating it based on EST analysis. The discovered splices are further analyzed to determine alternative splicing events. They have identified 6201 alternative splice relationships in human genes, through a genome-wide analysis of expressed sequence tags (ESTs). Starting with 2.1 million human mRNA and EST sequences, they mapped expressed sequences onto the draft human genome sequence and only accepted splices that obeyed the standard splice site consensus. After constructing a tissue list of 46 human tissues with 2 million human ESTs, they generated a database of novel human alternative splices that is four times larger than our previous report, and used Bayesian statistics to compare the relative abundance of every pair of alternative splices in these tissues. Using several statistical criteria for tissue specificity, they have identified 667 tissue-specific alternative splicing relationships and analyzed their distribution in human tissues. They have validated our results by comparison with independent studies. This genome-wide analysis of tissue specificity of alternative splicing will provide a useful resource to study the tissue-specific functions of transcripts and the association of tissue-specific variants with human diseases. | gene, genome, human, isoform, mechanism, metazoa, molecular, mrna, nucleus, process, protein, sequence, splice, tissue specificity, transcription, transcript, alternate splicing, microarray, alternative splicing, biological process, alternatively spliced isoform, contig, cancer, image |
is listed by: Biositemaps is related to: Alternative Splicing Annotation Project II Database has parent organization: University of California at Los Angeles; California; USA |
NSF 0082964; NSF DGE-9987641; DOE DEFG0387ER60615 |
PMID:12519958 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33105 | SCR_003415 | Alternative Splicing, Alternative Splicing Annotation Project, Alternative Splicing Annotation Project database | 2026-09-19 12:56:40 | 33 | |||||
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BIND Resource Report Resource Website 100+ mentions |
BIND (RRID:SCR_003576) | BIND | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. Designed to capture protein function, defined at molecular level as set of other molecules with which protein interacts or reacts along with molecular outcome. Archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view and submit records. BIND continues to grow with the addition of individual submissions as well as interaction data from the PDB and a number of large-scale interaction and complex mapping experiments using yeast two hybrid, mass spectrometry, genetic interactions and phage display. | interaction, protein, protein-protein interaction, small molecule-protein, nucleic acid-protein, small molecule, nucleic acid |
is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: Christopher Hogues Research Lab at the National University of Singapore is related to: MPIDB is related to: PSICQUIC Registry is related to: Agile Protein Interactomes DataServer works with: IMEx - The International Molecular Exchange Consortium |
PMID:12519993 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_11393 | http://bind.ca/ | SCR_003576 | Biomolecular Interaction Network Database | 2026-09-19 12:56:40 | 181 | |||||
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FlyTF.org Resource Report Resource Website 10+ mentions |
FlyTF.org (RRID:SCR_004123) | FlyTF | data or information resource, database | A database of genomic and protein data for Drosophila site-specific transcription factors. | transcription factor, gene, annotation, genome, protein |
is listed by: OMICtools has parent organization: MRC Laboratory of Molecular Biology |
PMID:16613907 | The community can contribute to this resource, Acknowledgement requested | OMICS_00534 | SCR_004123 | FlyTF.org - The Drosophila Transcription Factor Database | 2026-09-19 12:56:41 | 12 | ||||||
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LINCS Information Framework Resource Report Resource Website 1+ mentions |
LINCS Information Framework (RRID:SCR_003937) | data or information resource, database | LIFE search engine contains data generated from LINCS Pilot Phase, to integrate LINCS content leveraging semantic knowledge model and common LINCS metadata standards. LIFE makes LINCS content discoverable and includes aggregate results linked to Harvard Medical School and Broad Institute and other LINCS centers, who provide more information including experimental conditions and raw data. Please visit LINCS Data Portal. | bioassay, cell, small molecule, kinase protein, compound, cell, gene, metadata standard, cell line, primary cell, rnai reagent, rnai, reagent, protein reagent, protein, antibody reagent, antibody, perturbagen, growth factor, ligand, linked data, organ, disease, data set |
uses: HMS LINCS Database uses: Bioassay Ontology uses: Molecular Libraries Program is related to: Broad Institute is related to: Harvard Medical School; Massachusetts; USA is related to: Columbia University; New York; USA is related to: Yale University; Connecticut; USA is related to: Arizona State University; Arizona; USA has parent organization: University of Miami; Florida; USA |
NHGRI ; NHLBI U01 HL111561 |
PMID:29140462 | Free, Freely available | nlx_158348 | http://dev3.ccs.miami.edu:8080/datasets-beta/ | http://lifekb.org/ | SCR_003937 | lifekb, LIFE LINCS Information Framework | 2026-09-19 12:56:41 | 1 | ||||
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3DSwap Resource Report Resource Website 1+ mentions |
3DSwap (RRID:SCR_004133) | data or information resource, database | Curated knowledegbase of protein structures that are reported to be involved in 3-dimensional domain swapping. 3DSwap provides literature curated information and structure related information about 3D domain swapping in proteins. Information about swapping, hinge region, swapped region, extent of swapping, etc. are extracted from original research publications after extensive literature curation. | protein structure, protein, structure, 3d domain swapping, function, sequence, domain swap, 3d spatial image | has parent organization: Tata Institute of Fundamental Research; Mumbai; India | Tata Institute of Fundamental Research; Mumbai; India ; National Centre for Biological Sciences ; Wellcome Trust |
PMID:21959866 PMID:21592079 |
nlx_143564 | SCR_004133 | 3DSwap: Knowledgebase of 3D Domain Swapping in Proteins, 3DSwap - Knowledgebase of proteins involved in 3D domain swapping, 3D Swap, 3DSwap Database | 2026-09-19 12:56:41 | 5 | |||||||
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IntegromeDB Resource Report Resource Website 1+ mentions |
IntegromeDB (RRID:SCR_004620) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016. Search engine that integrates over 100 curated and publicly contributed data sources and provides integrated views on the genomic, proteomic, transcriptomic, genetic and functional information currently available. Information featured in the database includes gene function, orthologies, gene expression, pathways and protein-protein interactions, mutations and SNPs, disease relationships, related drugs and compounds. | catalog, search engine, gene, protein, gene regulation, gene expression, protein-protein interaction, pathway, metagenomics, mutation, disease, transcriptional regulation, genomics, transcriptomics, genetics, function, interaction, ortholog |
is related to: ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters has parent organization: University of California at San Diego; California; USA |
NIH ; NIGMS R01 GM084881 |
PMID:22260095 PMID:20427517 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_63198 | SCR_004620 | Integrome DB | 2026-09-19 12:56:45 | 3 | ||||||
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AmphoraNet Resource Report Resource Website 10+ mentions |
AmphoraNet (RRID:SCR_005009) | AmphoraNet | analysis service resource, data analysis service, production service resource, service resource | Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data. It is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample. | dna sequence, amino acid sequence, dna, sequence, amino acid, phylogenetic, reliability score, nucleotide, protein, nucleotide sequence, protein sequence, phylogenetic analysis, metagenomic, metagenomics, phylotyping, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Eotvos Lorand University; Budapest; Hungary |
PMID:24144838 | Acknowledgement requested, Free, Public | biotools:amphoranet, OMICS_01450 | https://bio.tools/amphoranet | SCR_005009 | 2026-09-19 12:56:48 | 16 |
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