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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
Cerebellar Development Transcriptome Database
 
Resource Report
Resource Website
1+ mentions
Cerebellar Development Transcriptome Database (RRID:SCR_013096) CDT-DB data or information resource, database, atlas Transcriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains. gene expression, fluorescence, function, gene, gene chip, genome, bioinformatics, brain, cell, cerebellum, development, in situ hybridization, fluroescence differential display, cerebellar development, microarray, mining, mouse, mrna, ontology, pathway, protein, rt-pcr, molecular neuroanatomy resource, transcriptiome, spatiotemporal, cdna microarray, genechip, postnatal, histochemistry, image, postnatal development is related to: Gene Ontology
is related to: RIKEN integrated database of mammals
has parent organization: RIKEN Brain Science Institute
Brain development, Brain disorder INCF Japan Node ;
Japan Society for the Promotion of Science ;
Japanese Ministry of Education Culture Sports Science and Technology MEXT ;
Japan Science and Technology Agency
PMID:18603407 To be used for research and educational purposes only. Any reproduction or use for commercial purposes is prohibited without the prior express written permission of the RIKEN. nif-0000-00008 SCR_013096 2026-07-28 09:43:13 1
Biological Interaction database for Protein-nucleic Acid
 
Resource Report
Resource Website
Biological Interaction database for Protein-nucleic Acid (RRID:SCR_013371) BIPA data or information resource, database A database for protein-nucleic acid interaction that provides various features of protein-nucleic acid interfaces.
There are 2333 protein-nucleic acid PDB complexes, 9547 SCOP domains, and 9633 domain-nucleic acid interfaces in BIPA. BIPA also provides a multiple structural alignment of representative structures at the SCOP family level using the program SALIGN, and the structural alignments were further annotated using the program JOY to detect local environments of amino acids.
amino acid, interaction, nucleic acid, protein has parent organization: University of Cambridge; Cambridge; United Kingdom nif-0000-20819 http://www-cryst.bioc.cam.ac.uk/bipa SCR_013371 Biological Interaction database for Protein-nucleic Acid 2026-07-28 09:43:13 0
doRiNA
 
Resource Report
Resource Website
10+ mentions
doRiNA (RRID:SCR_013222) doRiNA data or information resource, database In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions. binding site, rna binding protein, microrna, post-transcription, rna, gene, genome, mammal, population variation, gene expression, transcript, regulator, protein, binding is related to: UCSC Genome Browser
has parent organization: Max Delbruck Center for Molecular Medicine; Berlin; Germany
MDC Systems Biology Network ;
BMBF ;
Senate of Berlin; Berlin; Germany ;
DFG
PMID:22086949 nlx_151321, r3d100011087 SCR_013222 2026-07-28 09:43:14 15
FlyTrap- GFP Protein Trap Database
 
Resource Report
Resource Website
10+ mentions
FlyTrap- GFP Protein Trap Database (RRID:SCR_013354) data or information resource, database The FlyTrap database presents the current results of large scale protein trapping screens that provide both information on which cells express each tagged gene, and subcellular localization of GFP-tagged proteins. Expression is under the control of endogenous promoter and enhancer elements, allowing for visualization of normal expression patterns. Drosophila proteins tagged with Green Fluorescent Protein (GFP) were created by insertion into genes of an artificial exon encoding GFP flanked by splice acceptor (SA) and splice donor (SD) sequences so that expression of GFP relies on splicing into mature mRNAs and in-frame fusion. gfp-tagged protein, protein, protein trapping screen has parent organization: Yale University; Connecticut; USA nif-0000-02849 SCR_013354 FlyTrap 2026-07-28 09:43:15 26
Drosophila melanogaster Exon Database
 
Resource Report
Resource Website
1+ mentions
Drosophila melanogaster Exon Database (RRID:SCR_013441) DEDB data or information resource, database Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers. exon, gene, alternative splicing, annotation, classification, cluster, domain, genome, graph, homology, protein, splicing, structure, transcript, visualize, blast is listed by: OMICtools
is related to: FlyBase
has parent organization: National University of Singapore; Singapore; Singapore
Agency for Science Technology and Research PMID:15581431 nif-0000-21118, OMICS_01894 SCR_013441 DEDB - Drosophila melanogaster Exon Database, DEDB : Drosophila melanogaster Exon Database 2026-07-28 09:43:29 2
RARTF
 
Resource Report
Resource Website
1+ mentions
RARTF (RRID:SCR_013457) RARTF data or information resource, database Database of complete sets of Arabidopsis transcription factors with a variety of information on Arabidopsis thaliana transcription factor families including: full-length cDNA sequences, Ds-tagged mutants, multiple sequences alignments of family members, phylogenic trees, functional motifs, and so on. In addition, expression profiles of all transcription factor genes are available. transcription factor, protein, gene, microarray, expression profile is listed by: OMICtools
is related to: InterProScan
PMID:16769687 Free OMICS_00562 SCR_013457 RARTF: RIKEN Arabidopsis Transcription Factor database, RIKEN Arabidopsis Transcription Factor database 2026-07-28 09:43:14 2
Embassy-domsearch
 
Resource Report
Resource Website
Embassy-domsearch (RRID:SCR_016086) software toolkit, source code, software resource Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt. dhf, daf, redundancy, protein, domain, psi-blast, uniprot, molecular, biology is used by: RAVEN
is listed by: Debian
Free, Available for download, Freely available https://sources.debian.org/src/embassy-domsearch/ SCR_016086 2026-07-28 09:44:08 0
Mass Spectral Library
 
Resource Report
Resource Website
10+ mentions
Mass Spectral Library (RRID:SCR_014668) data or information resource, database A library containing spectra upwards of 200,000 chemical compounds. Spectra include metabolites, peptides, contaminants, and lipids. All spectra and chemical structures are examined by professionals. library, database, spectra, mass spectrometry, metabolomics, metabolites, protein, lipid, contaminant is listed by: Metabolomics Workbench Available with the NIST MS Search Program for Windows SCR_014668 2026-07-28 09:43:31 18
Viral Integrated Structural Evolution Dynamic Database
 
Resource Report
Resource Website
1+ mentions
Viral Integrated Structural Evolution Dynamic Database (RRID:SCR_018793) VIStEDD data or information resource, database Database of SARS-CoV-2 and other viruses. Integrates structural and dynamic insights with viral evolution for proteins coded by virus. Each virus within database has workflow performed on each protein. Workflow consists of protein modeling, molecular dynamic simulations, evolutionary analysis, and mapping of protein-protein interactions. On page for each protein is link to individual protein data folder system, video of protein rotating with conservation, details of protein function, widget to purchase 3D print of protein at cost of production, amino acid movement from molecular dynamic simulations, and table of data for each amino acid of protein. Virus, SARS-CoV-2, COVID-19, proteins coded by virus, viral evolution, protein, data, amino acid, protein modeling, molecular dynamic simulation, evolutionary analysis, protein-protein interaction, protein- protein interaction mapping, protein data folder system, rotating protein video, protein function, molecular dynamic simulation has parent organization: Michigan State University; Michigan; USA COVID-19 NIGMS R01 GM108618;
NIEHS K01 ES025435
PMID:32511397 Free, Freely available SCR_018793 Viral Integrated Structural Evolution Dynamic Database, SARS-CoV-2 dynamicome database 2026-07-28 09:44:45 3
EPSD Eukaryotic Phosphorylation Site Database
 
Resource Report
Resource Website
1+ mentions
EPSD Eukaryotic Phosphorylation Site Database (RRID:SCR_016514) EPSD data or information resource, database Software tool as an annotated database of protein phosphorylation sites in eukaryotes. Contains experimentally identified and conserved p-sites which were collected from phosphoproteomic studies. protein, phosphorylation, site, eukaryotes, phosphoproteomic, data has parent organization: Huazhong University of Science and Technology; Wuhan; China Special Project on Precision Medicine under the National Key R&D Program 2017YFC0906600;
the Natural Science Foundation of China 31671360;
the Fundamental Research Funds for the Central Universities 2017KFXKJC001
Free, Freely available SCR_016514 Eukaryotic Phosphorylation Site Database, EPSD 2026-07-28 09:44:20 1
SRMAtlas
 
Resource Report
Resource Website
1+ mentions
SRMAtlas (RRID:SCR_016996) SRM Atlas, SRMatlas data or information resource, database, atlas 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 ;
NHGRI RC2 HG005805;
NIGMS R01 GM087221;
NCRR S10 RR027584;
NIGMS P50 GM076547;
Luxembourg Centre for Systems Biomedicine University Luxembourg ;
European Research Council ;
Swiss National Science Foundation
PMID:27453469 Publicly available, Registration required SCR_016996 2026-07-28 09:44:27 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 2026-07-28 09:44:37 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 2026-07-28 09:40:00 0
Windber Tissue Bank
 
Resource Report
Resource Website
Windber Tissue Bank (RRID:SCR_000509) WRI Tissue Bank tissue bank, biomaterial supply resource, material resource 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 2026-07-28 09:40:00 0
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 2026-07-28 09:39:59 0
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 2026-07-28 09:39:55 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 2026-07-28 09:40:04 2
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 2026-07-28 09:40:04 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 2026-07-28 09:40:04 1
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 2026-07-28 09:40:05 4

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