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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
SRMAtlas
 
Resource Report
Resource Website
1+ mentions
SRMAtlas (RRID:SCR_016996) SRM Atlas, SRMatlas atlas, data or information resource, database Resource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome. collection, proteomic, assay, detect, quantify, protein, mass, spectrometry, peptide American Recovery and Reinvestment Act ;
European Research Council ;
Luxembourg Centre for Systems Biomedicine University Luxembourg ;
NCRR S10 RR027584;
NHGRI RC2 HG005805;
NIGMS P50 GM076547;
NIGMS R01 GM087221;
Swiss National Science Foundation
PMID:27453469 Publicly available, Registration required SCR_016996 2026-09-05 06:32:14 3
ALZPEDIA
 
Resource Report
Resource Website
1+ mentions
ALZPEDIA (RRID:SCR_017548) AlzPedia data or information resource, database Collection of brief summaries of various genes and proteins implicated in pathophysiology of Alzheimer’s disease and other neurodegenerative disorders. It will be expanded over time and updated periodically in order to reflect current state of knowledge. Summary, gene, protein, pathophysiology, Alzheimer, neurodegenerative, disorder is related to: Alzheimer's Research Forum Free, Freely available SCR_017548 2026-09-05 06:32:15 3
eSLDB - eukaryotic Subcellular Localization database
 
Resource Report
Resource Website
1+ mentions
eSLDB - eukaryotic Subcellular Localization database (RRID:SCR_000052) eSLDB data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions. proteome, protein, homology has parent organization: University of Bologna; Bologna; Italy European Union VI Framework Programme PMID:17108361 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-02815 SCR_000052 eukaryotic Subcellular Localization database 2026-09-05 06:31:09 1
Interolog/Regulog Database
 
Resource Report
Resource Website
1+ mentions
Interolog/Regulog Database (RRID:SCR_000755) data or information resource, database Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins. interacting, interolog, protein, regulog, sequence, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Yale University; Connecticut; USA
PMID:15173116 nif-0000-20863, biotools:interolog https://bio.tools/interolog SCR_000755 Interolog 2026-09-05 06:31:12 2
ARNIE
 
Resource Report
Resource Website
ARNIE (RRID:SCR_000514) ARNIE data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided. network, orthologue, paralogue, gene, orthologue, protein interaction, protein, blast, extracellular, expression profiling, interaction network, ligand, interaction, signaling is listed by: OMICtools
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
MRC ;
Wellcome Trust
PMID:20802085 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01529 SCR_000514 AVEXIS Receptor Network with Integrated Expression 2026-09-05 06:31:10 0
Windber Tissue Bank
 
Resource Report
Resource Website
Windber Tissue Bank (RRID:SCR_000509) WRI Tissue Bank biomaterial supply resource, material resource, tissue bank Under the direction of Stella Somiari, Ph.D., the tissue bank at Windber Research Institute acquires and banks large numbers of high quality and well annotated normal and diseased tissue specimens. These specimens are obtained from fully informed and consented donors using Institutional Review Board (IRB) approved protocols and are accompanied by detailed clinical, family history and demographic information. The tissue bank has established Standard Operating Procedures (SOPs) for tissue acquisition, handling, processing, packaging and shipping. All collaborators at participating clinics/medical centers utilize these procedures to ensure that the integrity of the specimen is maintained. Tissue types in our collection include plasma, serum, tissue embedded in optimum cutting temperature (OCT), formalin fixed paraffin embedded, and flash frozen. We also isolate and bank tissue derived products such as DNA, RNA and protein for research. Very stringent SOPs are in place for the process of extraction of these tissue-derived products and for quality control/quality assurance (QA/QC). The WRI tissue bank currently has 5 isothermal freezers each with the capacity to store 36,000 specimens. For all specimens obtained from surgical procedures, routine histology is performed to obtain representative Hematoxylin and Eosin (H & E) stained sections for imaging/archiving. All H & E sections are imaged on the Trestle SL-50 imaging system and these images are available online to designated collaborative sites. A certified pathologist verifies all tissue specimens and WRI has telepathology capabilities, which can also be utilized for pathology verification when a second pathologist opinion is required to confirm specimen diagnosis. Other uses of the telepathology capabilities include the verification of Laser Capture Microdissection (LCM) sections (by pathologist) to ensure the correct areas are captured for research. The telepathology system at WRI is the Trestle Corporation's Medmicro system, which permits the pathologist to remotely view, navigate and share images at sub-micron resolution over standard internet connections in real-time. specimen, clinical data, family history, demographic data, tissue, plasma, serum, dna, rna, protein, optimum cutting temperature, formalin fixed paraffin embedded, frozen, normal, disease is listed by: One Mind Biospecimen Bank Listing
has parent organization: Windber Research Institute
Normal, Disease THIS RESOURCE IS NO LONGER IN SERVICE nlx_29009 SCR_000509 Windber Research Institute Tissue Bank, Windber Research Institute Tissue Banking, Windber Tissue Banking, WRI Tissue Banking 2026-09-05 06:31:10 0
ProGlycProt
 
Resource Report
Resource Website
1+ mentions
ProGlycProt (RRID:SCR_000622) ProGlycProt data or information resource, database Manually curated, comprehensive repository of experimentally characterized bacterial glycoproteins and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused effort to provide concise relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, their glycosylating enzyme(s), glycosylation linked genes, and genomic context thereof, in a cross-referenced manner. The database is arranged into two sections namely, ProCGP and ProUGP. ProCGP is the main section containing characterized prokaryotic glycoproteins, defined as entries with at least one experimentally known glycosylated residue (glycosite). Whereas, ProUGP is the supplementary section, presenting uncharacterized prokaryotic glycoproteins, defined as entries with experimentally identified glycosylation but unidentified glycosites. The ProGlycProt has been developed with to aid and advance the emerging scientific interests in understanding the mechanisms, implications, and novelties of protein glycosylation in prokaryotes that include many pathogenic as well as economically important bacterial species. The website supports a dedicated structure gallery of homology models and crystal structures of characterized glycoproteins in addition to two new tools developed in view of emerging information about prokaryotic sequons (conserved sequences of amino acids around glycosites) that are never or rarely seen in eukaryotic glycoproteins. ProGlycProt provides an extensive compilation of experimentally identified glycosites (334) and glycoproteins (340) of prokaryotes that could serve as an information resource for research and technology applications in glycobiology. A general data update policy is once in three months. Existing entries are updated in real-time. glycoprotein, glycosite, glycosylation, coding gene, protein, glycosylation type, attached glycan, oligosaccharyl transferase, glycosyl transferase, glycobiology, glycosylating enzyme, glycosylation linked gene, crystal structure, homology, homology model, blast, predict, bacteria, archaea, image collection, structure, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Institute of Microbial Technology; Chandigarh; India
Institute of Microbial Technology; Chandigarh; India OLP0063;
Council of Scientific and Industrial Research; New Delhi; India SIP10AA
PMID:22039152 nlx_151583, biotools:proglycprot https://bio.tools/proglycprot SCR_000622 Prokaryotic Glycoproteins, ProGlycProt - A Repository of Experimentally Characterized GlycoProteins of Prokaryotes 2026-09-05 06:31:11 1
Protein-Protein Interactions Table for Human herpesvirus 1
 
Resource Report
Resource Website
Protein-Protein Interactions Table for Human herpesvirus 1 (RRID:SCR_000397) data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. The scope of the project includes molecular information pertaining to oral pathogens, bacterial and viral. The website contains a table of protein-protein interactions for human herpesvirus 1. It is operated for the U.S. Department of Energy's National Nuclear Security Administration. bacterial, herpesvirus 1, pathogen, protein, viral THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-20905 http://semiglobe.lanl.gov/microbe.php?class=virus SCR_000397 HSV1 PPI 2026-09-05 06:31:10 0
Biozon
 
Resource Report
Resource Website
1+ mentions
Biozon (RRID:SCR_000725) data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Biozon is a unified biological resource on DNA sequences, proteins, complexes and cellular pathways. It currently provides data on pairwise similarities between proteins, the domain structure of proteins, structural similarities, threading-based and profile-profile similarities between protein families. Additional information about 3D models, predicted protein-protein interactions, assignment of genes to pathways and expression data analysis, as well as local and global maps of the protein space will be gradually added to Biozon. 3d modelprotein-protein interaction, cellular pathway, dna sequence, protein, protein complex, protein family has parent organization: Stanford University; Stanford; California PMID:16381854
PMID:16480510
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-02613 SCR_000725 Biozon 2026-09-05 06:31:11 4
Collecting Duct Database
 
Resource Report
Resource Website
Collecting Duct Database (RRID:SCR_000759) CDDB data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. This database is intended to serve as a learning tool to obtain curated information for the design of microarray targets to scan collecting duct tissues (human, rat, mouse). The database focuses on regulatory and transporter proteins expressed in the collecting duct, but when collecting duct proteins are a member of a larger family of proteins, common additional members of the family are included even if they have not been demonstrated to be expressed in the collecting duct. An Internet-accessible database has been devised for major collecting duct proteins involved in transport and regulation of cellular processes. The individual proteins included in this database are those culled from literature searches and from previously published studies involving cDNA arrays and serial analysis of gene expression (SAGE). Design of microarray targets for the study of kidney collecting duct tissues is facilitated by the database, which includes links to curated base pair and amino acid sequence data, relevant literature, and related databases. Use of the database is illustrated by a search for water channel proteins, aquaporins, and by a subsequent search for vasopressin receptors. Links are shown to the literature and to sequence data for human, rat, and mouse, as well as to relevant web-based resources. Extension of the database is dynamic and is done through a maintenance interface. This permits creation of new categories, updating of existing entries, and addition of new ones. CDDB is a database that organizes lists of genes found in collecting duct tissues from three mammalian species: human, rat, and mouse. Proteins are divided into categories by family relationships and functional classification, and each category is assigned a section in the database. Each section includes links to the literature and to sequence information for genes, proteins, expressed sequence tags, and related information. The user can peruse a section or use a search engine at the bottom of the web page to search the database for a name or abbreviation or for a link to a sequence. Each entry in the database includes links to relevant papers in the kidney and collecting duct literature. It uses links to PubMed to generate MEDLINE searches for retrieval of references. In addition, each entry includes links to curated sequence data available in LocusLink. Individual links are made to sequence and protein data for human, rat, and mouse. Links are then added as curated sequences become available for proteins identified in the renal collecting duct and for proteins identified in kidney and similar in function or homologous to proteins identified in the collecting duct. expressed sequence tag, expression, family, functional, gene, aquaporin, array, cdna, classification, collecting duct, homologous, human, kidney, literature, mammal, mammalian, microarray, mouse, protein, protein localization and targeting databases, rat, receptor, regulatory, relationship, scan, serial analysis, specie, target, tissue, transporter, vasopressin, water channel protein has parent organization: National Institutes of Health THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-21078 SCR_000759 Collecting Duct Database 2026-09-05 06:31:12 0
MS Bioworks
 
Resource Report
Resource Website
MS Bioworks (RRID:SCR_001043) analysis service resource, data analysis service, production service resource, service resource A protein mass spectrometry service provider that delivers data to industrial and government organizations as well as academic institutions. Protein services include protein identification, mapping, profiling, and mass measurement. Post-translational modification services include PTM profiling, phospho-screening, and glyco-screening. Quantitative proteomics services include workflows for label free, TMT, SILAC, and PRM. MS Bioworks also provides immunoprecipitated protein analysis and custom analysis. mass spectrometry, protein, data, biomarkers, glycoproteins, proteomics service, analysis service resource, post translational modification, quantitative proteomics is listed by: ScienceExchange Services available for purchase SciEx_4856 http://www.scienceexchange.com/facilities/ms-bioworks SCR_001043 MS Bioworks - Protein Mass Spectrometry Services 2026-09-05 06:31:13 0
BLASTP
 
Resource Report
Resource Website
100+ mentions
BLASTP (RRID:SCR_001010) analysis service resource, data analysis service, production service resource, service resource Data analysis service whose programs search protein databases using a protein query. The algorithms used include blastp, psi-blast, phi-blast, and delta-blast. blast, basic local alignment search tool, protein alignment, protein blast, data analysis service, protein is used by: Open Reading Frame Finder
is listed by: OMICtools
is listed by: SoftCite
has parent organization: NCBI
Freely available, Acknowledgement requested OMICS_00991 SCR_001010 blastp suite, Standard Protein BLAST 2026-09-05 06:31:12 293
WegoLoc
 
Resource Report
Resource Website
1+ mentions
WegoLoc (RRID:SCR_001402) WegoLoc analysis service resource, data analysis service, production service resource, service resource Data analysis service that predicts protein subcellular localizations of animal, fungal, plant, and human proteins based on sequence similarity and gene ontology information. subcellular localization, protein is listed by: OMICtools
is related to: Gene Ontology
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01636 SCR_001402 weighted gene ontology term based subcellular locallization prediction 2026-09-05 06:31:13 4
MINT
 
Resource Report
Resource Website
1000+ mentions
MINT (RRID:SCR_001523) MINT data or information resource, database A database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them. protein-protein interaction, protein, interaction, virus, peptide, organelle co-localization, pathway, molecular interaction, papillomavirus, epstein-barr virus, hepatitis b virus, hepatitis c virus, human adenovirus, human herpesvirus, human immunodeficiency virus, influenza a virus, vaccinia virus, simian virus 40, virus strains, virus protein, orthologous protein, network, proteomics, ortholog, FASEB list uses: IntAct
uses: PSI-MI
is listed by: re3data.org
is affiliated with: IMEx - The International Molecular Exchange Consortium
is related to: MPIDB
is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions
is related to: InteroPorc
is related to: Interaction Reference Index
is related to: Pathway Commons
is related to: ConsensusPathDB
is related to: VirusMINT
is related to: PSICQUIC Registry
is related to: Agile Protein Interactomes DataServer
has parent organization: University of Rome Tor Vergata; Rome; Italy
works with: IMEx - The International Molecular Exchange Consortium
European Union ;
ENFIN ;
Interaction Proteome Project ;
IMEx - The International Molecular Exchange Consortium ;
HUPO Proteomics Standards Initiative ;
AIRC Associazione Italiana per la Ricerca sul Cancro
PMID:22096227
PMID:24234451
PMID:19897547
PMID:18592188
PMID:18551417
PMID:18428712
PMID:17135203
PMID:11911893
nlx_152821, r3d100010414 https://doi.org/10.17616/R38S3B SCR_001523 MINT, the Molecular INTeraction database, Molecular Interactions Database, Molecular INTeraction database, MINT - the Molecular INTeraction database 2026-09-05 06:31:14 1141
Protein interaction and molecular information database
 
Resource Report
Resource Website
Protein interaction and molecular information database (RRID:SCR_002096) data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. PRIME is a developed version of Kinase Pathway Database which is an integrated database concerning completed sequenced major eukaryotes, which contains the classification of protein kinases and their functional conservation and orthologous tables among species, protein-protein interaction data, domain information, structural information, and automatic pathway graph image interface. The protein-protein interactions are extracted by natural language processing (NLP) from abstracts using basic word pattern and protein name dictionary GENA: developed by our group. In this system, pathways are easily compared among species using protein interactions data more than 1,510,000 and orthologous tables. Further, using other organisms interaction data, interaction prediction is also possible. eukaryote, kinase pathway, protein, structure THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-20899 http://prime.ontology.ims.u-tokyo.ac.jp:8081/ SCR_002096 PRIME 2026-09-05 06:31:16 0
pSTIING
 
Resource Report
Resource Website
1+ mentions
pSTIING (RRID:SCR_002045) pSTIING data or information resource, database A publicly accessible knowledgebase about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. The knowledgebase allowing users to search and to dynamically generate visual representations of protein-protein interactions and transcriptional regulatory networks. Signalling and transcriptional modules can also be displayed singly or in combination. This allow users to identify important "cross-talks" between signalling modules via connections with key components or "hubs". The knowledgebase will facilitate a "systems-wide" understanding across many protein, signalling and transcriptional regulatory networks triggered by multiple environmental cues, and also serve as a platform for future efforts to computationally and mathematically model the system behavior of inflammatory processes and tumourigenesis. protein-protein, protein-lipid, protein-small molecule, ligand-receptor interaction, receptor-cell type, transcriptional regulatory module, signal transduction module, inflammation, cell migration, tumorigenesis, protein-protein interaction, transcriptional regulatory network, signalling pathway, interaction, protein interaction, motif, domain, protein, gene is listed by: OMICtools
is related to: Gene Ontology
has parent organization: University College London; London; United Kingdom
Inflammation, Tumor, Cancer PMID:16381926 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01916 SCR_002045 Protein Signalling Transcriptional Interactions and Inflammation Networks Gateway, Protein Signalling Transcriptional Interactions & Inflammation Networks Gateway 2026-09-05 06:31:15 2
Alignable Tight Genomic Cluster
 
Resource Report
Resource Website
1+ mentions
Alignable Tight Genomic Cluster (RRID:SCR_001894) ATGC data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. ATGC stands for Alignable Tight Genomic Cluster, which is cluster of closely related prokaryotic genomes. ATGC is the principal notion of this web resource. The purpose of this web resource is to prepare ATGC-derived data sets for a variety of research projects in functional and evolutionary genomics. Unique features of ATGC include: * Reliable identification of orthologs (high degree of similarity between the genomes in the set allow an extensive use of synteny in ortholog identification); * Fine granularity of protein classification (in comparisons of more distant genomes, proteins belonging to families of paralogs are often lumped into a singlegroup; under the ATGC approach, comparison of genomic sequences from highly similar genomes allows one to track each set of orthologs separately); * Relative rarity of changes of any kind (in sequence, genome organization and gene content) allows the use of parsimony-related methods of analysis. gene, genomic cluster, genomic sequence, ortholog, paralog, prokaryotic genomic, protein, protein classification has parent organization: Lawrence Berkeley National Laboratory Department of Energy Joint Genome Institute ;
NLM ;
DOE DE-AC02-05CH11231
PMID:28053163
PMID:18845571
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-02581 SCR_001894 2026-09-05 06:31:15 1
Subtilis Protein interaction Database
 
Resource Report
Resource Website
Subtilis Protein interaction Database (RRID:SCR_002123) SPiD data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. An online database of two-hybrid protein interactions in B. Subtilis. Interactions stored in SPID are either characterized by experimental evidence or by bibliographic references. A graphical user interface is provided to explore interaction networks as well as to view the details of each piece of evidence. The database contains 112 interactions between 79 proteins. b. subtilis, protein, protein interaction THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-20916 SCR_002123 Subtilis Protein interaction Database 2026-09-05 06:31:16 0
PubGene
 
Resource Report
Resource Website
10+ mentions
PubGene (RRID:SCR_002119) data or information resource, database It helps users retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a gene-centric database. Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances. The result is a literature network organizing information in a form that is easy to navigate. gene, information, protein, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
is parent organization of: Coremine Medical
Free, Freely Available biotools:pubgene, nif-0000-20908 https://bio.tools/pubgene SCR_002119 PubGene 2026-09-05 06:31:16 39
Conserved Domain Database
 
Resource Report
Resource Website
100+ mentions
Conserved Domain Database (RRID:SCR_002077) CDD data or information resource, database Database of annotations of functional units in proteins including multiple sequence alignment models for ancient domains and full-length proteins. This collection of models includes 3D structures that display the sequence/structure/function relationships in proteins. It also includes alignments of the domains to known three-dimensional protein structures in the MMDB database. The source databases are Pfam, Smart, and COG. Users can identify amino acids in protein sequences with the resources available as well as view single sequences embedded within multiple sequence alignments. protein, amino acid sequence, nucleic acid, 3d structure, annotation, function, sequence, structure, amino acid, gold standard is used by: Mutation Annotation and Genomic Interpretation
is listed by: re3data.org
is related to: Pfam
is related to: SMART
is related to: COG
is related to: NCBI Structure
has parent organization: NCBI
works with: Conserved Domains Search
PMID:25414356
PMID:18984618
nif-0000-02647, r3d100010653 http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd SCR_002077 Conserved Domains Database, Conserved Domains 2026-09-05 06:31:15 358

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