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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
GalaxyRefine
 
Resource Report
Resource Website
100+ mentions
GalaxyRefine (RRID:SCR_018531) web service, data access protocol, analysis service resource, software resource, production service resource, service resource Web server for protein structure prediction, refinement, and related methods. First rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation. Protein structure prediction, protein, structure prediction, protein structure, molecular dynamics simulation, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: Seoul National University; Seoul; South Korea
National Research Foundation of Korea ;
Seoul National University.
PMID:23737448 biotools:galaxyrefine https://bio.tools/galaxyrefine SCR_018531 2026-02-16 09:49:31 248
ToxinPred
 
Resource Report
Resource Website
100+ mentions
ToxinPred (RRID:SCR_018542) software toolkit, analysis service resource, software resource, production service resource, service resource Software package for peptides designing and prediction. In silico approach for predicting toxicity of peptides and proteins. Used for predicting peptide toxicity or non toxicity, minimum mutations in peptides for increasing or decreasing their toxicity, toxic regions in proteins. Toxin, toxicity, toxicity prediction, peptide toxicity prediction, peptide design, protein, peptide mutation, toxic region, protein toxic region Department of Biotechnology Govt. of India ;
Council of Scientific and Industrial Research Govt. of India
PMID:29300301 Free, Freely available SCR_018542 2026-02-16 09:49:29 161
Batch Web CD-Search Tool
 
Resource Report
Resource Website
100+ mentions
Batch Web CD-Search Tool (RRID:SCR_018756) service resource, data access protocol, software resource, web service Web tool for detection of structural and functional domains in protein sequences. Allows computation and download of conserved domain annotation for large sets of protein queries. Allows to view results graphically. Shows domain footprints, alignment details, and conserved features on any individual query sequence. Functional domain detection, protein sequence, protein sequence domain, functional domain, protein, nucleotide sequence, conserved domain search, bio.tools is listed by: Debian
is listed by: bio.tools
NIH Intramural Research Program PMID:15215404 Free, Freely available biotools:cd-search https://bio.tools/cd-search SCR_018756 NCBI Batch CD Search Tool, Batch conserved domain search, Conserved Domain Search service, CD-search 2026-02-16 09:49:33 368
PPA-Pred2
 
Resource Report
Resource Website
1+ mentions
PPA-Pred2 (RRID:SCR_018957) software application, web service, data access protocol, software resource, simulation software Web server for protein protein affinity prediction. Used for predicting binding affinity of protein protein complexes. Protein, protein affinity, affinity prediction, predicting binding affinity, protein protein complex, binding affinity Department of Science and Technology ;
Government of India
PMID:5172924 Free, Freely available SCR_018957 Protein-Protein Affinity Predictor 2 2026-02-16 09:49:34 5
Vesiclepedia
 
Resource Report
Resource Website
100+ mentions
Vesiclepedia (RRID:SCR_019011) data repository, database, storage service resource, service resource, data or information resource Web based database of proteins, RNA, lipids and metabolites that are identified in extracellular vesicles. Compendium for extracellular vesicles with continuous community annotation and with manually curated data from published literature. Extracellular vesicles, gene information, molecule information, protein, RNA, lipid, metabolite, gene ontology, annotation, external references, FASEB list uses: Entrez Gene Australian Research Council ;
NHMRC project grant
DOI:10.1371/journal.pbio.1001450
DOI:10.1093/nar/gky1029
Free, Freely available SCR_019011 Vesiclepedia 2019 2026-02-16 09:49:34 149
FGENESH Plus
 
Resource Report
Resource Website
1+ mentions
FGENESH Plus (RRID:SCR_018937) software application, web service, data access protocol, software resource, simulation software Web tool as HMM plus similar protein based gene prediction. Used for multiple gene prediction in genomic DNA with using information from similar protein. Used if you know protein sequence similar with protein which is encoded by gene in your sequence. HMM, gene prediction, protein, multiple gene prediction, genomic DNA, similar protein, protein sequence, Softberry is related to: Fgenesh plus plus Free, Freely available SCR_018937 Fgenesh plus 2026-02-16 09:49:37 6
MSQuant
 
Resource Report
Resource Website
1+ mentions
MSQuant (RRID:SCR_019206) software application, data processing software, data analytics software, data analysis software, software resource Software tool for quantitative proteomics,mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.Entry in MSQuant is Mascot search engine. Qantitative proteomics, mass spectrometry, spectra processes, LC runs, protein, peptide uses: Mascot
is listed by: SoftCite
Free, Available for download http://msquant.alwaysdata.net/ SCR_019206 2026-02-16 09:49:42 4
NetNGlyc
 
Resource Report
Resource Website
1000+ mentions
NetNGlyc (RRID:SCR_001570) NetNGlyc software application, data analysis service, analysis service resource, software resource, production service resource, service resource Server that predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. NetNGlyc 1.0 is also available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms. predict, n-glycosylation site, human, protein, neural network, sequence, asn-xaa-ser/thr sequon, glycoprotein, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: CBS Prediction Servers
Free, Freely available nlx_153863, biotools:netnglyc https://bio.tools/netnglyc SCR_001570 NetNGlyc Server 2026-02-16 09:45:31 1753
YinOYang
 
Resource Report
Resource Website
100+ mentions
YinOYang (RRID:SCR_001605) YinOYang software application, data analysis service, analysis service resource, software resource, production service resource, service resource Server that produces neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences. This server can also use NetPhos, to mark possible phosphorylated sites and hence identify Yin-Yang sites. YinOYang 1.2 is available as a stand-alone software package, with the same functionality. Ready-to-ship packages exist for the most common UNIX platforms. neural network, prediction, o-beta-glcnac attachment site, protein sequence, protein, sequence, glycosylation site, proteome, post-translational modification, protein function, glycoprotein, bio.tools uses: NetPhos
is listed by: bio.tools
is listed by: Debian
has parent organization: CBS Prediction Servers
Danish National Research Foundation PMID:11928486 Free, Freely available nlx_153865, biotools:yinoyang https://bio.tools/yinoyang SCR_001605 2026-02-16 09:45:32 111
MatrixDB
 
Resource Report
Resource Website
50+ mentions
MatrixDB (RRID:SCR_001727) MatrixDB production service resource, service resource, data or information resource, database Freely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions. extracellular, protein fragment, biomolecule, cation, cleavage, collagen, glycosaminoglycan, human, interaction, laminin, lipid, mammalian, matricryptin, matrikin, matrix, molecule, monomer, mulimerization, multimer, polysaccharide, protein, protein-carbohydrate interaction, protein-protein interaction, recognition, thrombospondin, interactome, extracellular protein, protein-polysaccharide interaction, extracellular interaction, molecular interaction, model organism, inorganic, small molecule-protein, small molecule, extracellular matrix protein, protein-glycosaminoglycan interaction, bio.tools, FASEB list is listed by: re3data.org
is listed by: bio.tools
is listed by: Debian
is related to: IMEx - The International Molecular Exchange Consortium
is related to: Gene Ontology
is related to: PSI-MI
is related to: HPRD - Human Protein Reference Database
is related to: Interaction Reference Index
is related to: ConsensusPathDB
is related to: IMEx - The International Molecular Exchange Consortium
is related to: PSICQUIC Registry
is related to: IntAct
has parent organization: Claude Bernard University Lyon 1; Lyon; France
European Union contract FP7-HEALTH-2007-223411 PMID:20852260
PMID:19147664
THIS RESOURCE IS NO LONGER IN SERVICE biotools:matrixdb, r3d100010672, nif-0000-10226 https://bio.tools/matrixdb
https://doi.org/10.17616/R3M03H
http://matrixdb.ibcp.fr/ SCR_001727 MatrixDB: Extracellular Matrix Interactions Database, Extracellular Matrix Interactions Database 2026-02-16 09:45:36 86
Clustal Omega
 
Resource Report
Resource Website
5000+ mentions
Clustal Omega (RRID:SCR_001591) Clustal Omega, Clustalo software application, data processing software, image analysis software, software resource, service resource, alignment software Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF. multiple, sequence, alignment, DNA, RNA, protein, generate, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: Clustal W2
is related to: Clustal W2
is related to: Clustal 2
has parent organization: European Bioinformatics Institute
has parent organization: University College Dublin; Dublin; Ireland
Science Foundation Ireland PMID:21988835
PMID:20439314
DOI:10.1038/msb.2011.75
Free, Available for download, Freely available OMICS_00972, SCR_016062, biotools:clustalo, nlx_153836 https://sources.debian.org/src/clustalo/
http://www.clustal.org/omega/
http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::clustalO-multialign
https://bio.tools/clustalo
https://sources.debian.org/src/clustalo/
SCR_001591 2026-02-16 09:45:32 9956
Kidney and Urinary Pathway Knowledge Base
 
Resource Report
Resource Website
1+ mentions
Kidney and Urinary Pathway Knowledge Base (RRID:SCR_001746) KUPKB data set, data analysis service, analysis service resource, data repository, storage service resource, production service resource, service resource, data or information resource A collection of omics datasets (mRNA, proteins and miRNA) that have been extracted from PubMed and other related renal databases, all related to kidney physiology and pathology giving KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. Some microarray raw datasets have also been downloaded from the Gene Expression Omnibus and analyzed by the open-source software GeneArmada. The Semantic Web technologies, together with the background knowledge from the domain's ontologies, allows both rapid conversion and integration of this knowledge base. SPARQL endpoint http://sparql.kupkb.org/sparql The KUPKB Network Explorer will help you visualize the relationships among molecules stored in the KUPKB. A simple spreadsheet template is available for users to submit data to the KUPKB. It aims to capture a minimal amount of information about the experiment and the observations made. kidney, urinary, urine, pathway, molecule, visualizer, gene, protein, mirna, metabolite, mrna, microarray, ortholog, rdf, renal cell, anatomy, animal model, disease, sparql, proteomics, ontology, biomarker, gene expression, physiology, pathology is related to: NIDDK Information Network (dkNET)
is related to: Gene Expression Omnibus
is related to: Gene Ontology
is related to: KEGG
has parent organization: University of Manchester; Manchester; United Kingdom
has parent organization: National Institute of Health and Medical Research; Rennes; France
Kidney disease European Union ;
FP7 ;
ICT-2007.4.4 e-LICO project
PMID:21624162 THIS RESOURCE IS NO LONGER IN SERVICE. nlx_154134 http://www.e-lico.eu/kupkb SCR_001746 Kidney & Urinary Pathway Knowledge Base 2026-02-16 09:45:34 2
BLASTX
 
Resource Report
Resource Website
10000+ mentions
BLASTX (RRID:SCR_001653) BLASTX data analysis service, analysis service resource, database, production service resource, service resource, data or information resource Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level. protein, translated nucleotide, blast, nucleotide, expressed sequence tag, sequence, genome, wgs, peptide, alignment, dna is listed by: OMICtools
is listed by: SoftCite
has parent organization: NCBI
PMID:28902395
PMID:8485583
Free, Freely Available nlx_153933, OMICS_00992 http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome SCR_001653 Translated BLAST, Translated BLAST: blastx 2026-02-16 09:45:32 10091
Homology Maps Page
 
Resource Report
Resource Website
1+ mentions
Homology Maps Page (RRID:SCR_001666) data or information resource, topical portal, portal This page provides quick access to the Comparative mapping functions available in the Map Viewer. Currently, comparative maps are calculated using HomoloGene orthology predictions. Once the gene pairs have been established, blocks of conserved syteny can be established using the positions of each gene object in their respective builds. Sponsors: This resource is supported by NCBI. function, gene, comparative, homology, map, mapping, orthology, protein has parent organization: NCBI Free, Freely Available nif-0000-25559 SCR_001666 Homology 2026-02-16 09:45:33 2
Chilibot: Gene and Protein relationships from MEDLINE
 
Resource Report
Resource Website
10+ mentions
Chilibot: Gene and Protein relationships from MEDLINE (RRID:SCR_001705) Chilibot data analysis service, analysis service resource, database, production service resource, service resource, data or information resource Data analysis service that searches PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords using a NLP-based text-mining approach. The results are returned as a graph. The synonym database used in Chilibot is available, without fee, for academic use only. Several different search methods are supported including: * searching for relationship between two genes, proteins or keywords * searching for relationships between many genes, proteins, or keywords * searching for relationships between two lists of genes, proteins, or keywords Advanced options include: * Automated hypothesis generation (graph) * Restricting context using keywords * Providing your own synonyms * Modifying synonyms provided by Chilibot * Color coding nodes with gene expression values * Special search: modulation drug, gene, literature, natural language processing, protein, text-mining, network, keyword, biological concept, graph, bio.tools is listed by: OMICtools
is listed by: 3DVC
is listed by: bio.tools
is listed by: Debian
is related to: PubMed
has parent organization: University of Tennessee Health Science Center; Tennessee; USA
PHS DA-03977 PMID:15473905 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10196, OMICS_01176, biotools:chilibot https://bio.tools/chilibot SCR_001705 Chilibot - Mining PubMed for relationships 2026-02-16 09:45:35 30
International Union of Physiological Sciences: Physiome Project
 
Resource Report
Resource Website
1+ mentions
International Union of Physiological Sciences: Physiome Project (RRID:SCR_001760) data or information resource, topical portal, portal The Physiome Project is a worldwide public domain effort to provide a computational framework for understanding human and other eukaryotic physiology. It aims to develop integrative models at all levels of biological organization, from genes to the whole organism via gene regulatory networks, protein pathways, integrative cell function, and tissue and whole organ structure/function relations. Additionally, an important goal of the project is to develop applications for teaching physiology. Current projects include the development of: - ontologies to organize biological knowledge and access to databases - markup languages to encode models of biological structure and function in a standard format for sharing between different application programs and for re-use as components of more comprehensive models - databases of structure at the cell, tissue and organ levels - software to render computational models of cell function such as ion channel electrophysiology, cell signaling and metabolic pathways, transport, motility, the cell cycle, etc. in 2 & 3D graphical form - software for displaying and interacting with the organ models which will allow the user to move across all spatial scales Sponsors: This project is supported by the International Union of Physiological Sciences (IUPS), the IEEE Engineering. in Medicine and Biology (EMBS), and the International Federation for Medical and Biological Engineering (IFMBE) electrophysiology, eukaryotic, framework, function, gene, 3d form, biological, cell, cell cycle, channel, computational, human, ion, metabolic, model, motility, network, organ, organism, pathway, physiology, physiome, protein, public domain, regulatory, signaling, software, structure, tissue, transport is related to: Physiome Model Repository Free, Freely available nif-0000-10266 http://www.physiome.org.nz/ SCR_001760 IUPS Physiome 2026-02-16 09:45:36 2
DAVID
 
Resource Report
Resource Website
10000+ mentions
DAVID (RRID:SCR_001881) DAVID web service, data access protocol, database, software resource, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis. functional domain, annotation, motif, protein, ontology enrichment, gene, high-throughput, functional classification, functional annotation, clustering, genome, pathway, gene-disease association, interaction, functional domain, motif, visualization, FASEB list is listed by: OMICtools
is listed by: 3DVC
is listed by: LabWorm
is listed by: SoftCite
is related to: Gene Ontology
is related to: BioCarta Pathways
is related to: KEGG
has parent organization: NCI-Frederick
NIAID NO1-CO-56000;
NCI
PMID:19131956
PMID:12734009
PMID:35325185
PMID:22543366
PMID:17980028
PMID:17576678
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-30408, nif-0000-10451, OMICS_02220, SCR_003033 http://david.abcc.ncifcrf.gov/ SCR_001881 DAVID Bioinformatics Resources, Visualization and Integrated Discovery Bioinformatics Resources, Database for Annotation Visualization and Integrated Discovery, The Database for Annotation, The Database for Annotation Visualization and Integrated Discovery Bioinformatics Resources 2026-02-16 09:45:36 18488
University of Utah Genetic Science Learning Center - Learn Genetics
 
Resource Report
Resource Website
1+ mentions
University of Utah Genetic Science Learning Center - Learn Genetics (RRID:SCR_001910) Learn.Genetics, Learn Genetics video resource, narrative resource, training resource, training material, slide, data or information resource Educational resources that provide accurate and unbiased information about topics in genetics, bioscience and health for global and local audiences. They are jargon-free, target multiple learning styles, and often convey concepts through animation and interactivity. The Genetic Science Learning Center is a science and health education program located in the midst of the bioscience research being carried out at the University of Utah. Our mission is making science easy for everyone to understand. * Two websites, available free of charge to Internet users worldwide: ** Learn.Genetics delivers educational materials on genetics, bioscience and health topics. They are designed to be used by students, teachers and members of the public. The materials meet selected US education standards for science and health. ** Teach.Genetics provides resources for K-12 teachers, higher education faculty, and public educators. These include PDF-based Print-and-Go™ activities, unit plans and other supporting resources. The materials are designed to support and extend the materials on Learn.Genetics. *Professional development programs that update K-16 teachers' expertise in bioscience and health topics as well as prepare them to implement the materials on our websites. * Community programs that engage with diverse communities in discussions about genetics and health, and in developing culturally and linguistically-appropriate educational materials. Some topics in genetics and bioscience research are controversial. The Center does not take sides in political or ethical controversies. Rather, our goal is to provide comprehensive information that promotes a lively discussion of these topics, so that individuals can arrive at their own informed decisions. gene, dna, protein, education, genetics, science, bioscience, health, teacher, student, public, professional development, k-12, undergraduate, lesson plan, heredity, genetic trait, cell, molecule, stem cell, cloning, gene therapy, transgenic mouse, epigentics, addiction, genetic variation has parent organization: University of Utah; Utah; USA
is parent organization of: New Science of Addiction: Genetics and the Brain
NIH Office of the Director R25OD021903 You are granted a revocable license to download and print hard copy versions of the material contained on the site for your personal, Educational and noncommercial use, Provided you do not modify or delete any copyright or other notice that appears on the material you download or print. nif-0000-10482 http://learns.genetics.utah.edu/ SCR_001910 University of Utah Genetic Science Learning Center, Genetic Science Learning Center - Learn.Genetics, Genetic Science Learning Center, Genetic Science Learning Center - Learn Genetics 2026-02-16 09:45:36 9
Dynamic Brain Platform
 
Resource Report
Resource Website
1+ mentions
Dynamic Brain Platform (RRID:SCR_001754) DBPF data set, atlas, data repository, database, storage service resource, service resource, data or information resource, bibliography THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19. 2022. Platform to promote studies on dynamic principles of brain functions through unifying experimental and computational approaches in cellular, local circuit, global network and behavioral levels. Provides services such as data sets, popular research findings and articles and current developments in field. This site has been archived since FY2019 and is no longer updated. collaboration, glial cell, interaction, model, network, neuron, neuron-glia network, numerical tool, paper, protein, publish, tool, book, neural dynamics, brain, stimulus, book, conference, presentation, simulation, paper, simulator, experimental stimuli, poster, data sharing is related to: INCF Japan Node
has parent organization: RIKEN Brain Science Institute
Free, Freely available SCR_001812, nif-0000-10262, nif-0000-10377 https://nimg.neuroinf.jp/ SCR_001754 Neuro-Imaging Platform, Dynamic Brain PF 2026-02-16 09:45:34 1
MouseCyc
 
Resource Report
Resource Website
1+ mentions
MouseCyc (RRID:SCR_001791) MouseCyc data analysis service, analysis service resource, database, production service resource, service resource, data or information resource A manually curated database of both known and predicted metabolic pathways for the laboratory mouse. It has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 294 pathways with 1,790 compounds and 1,122 enzymatic reactions in MouseCyc. (Aug. 2013) BLAST and other tools are available. The initial focus for the development of MouseCyc is on metabolism and includes such cell level processes as biosynthesis, degradation, energy production, and detoxification. MouseCyc differs from existing pathway databases and software tools because of the extent to which the pathway information in MouseCyc is integrated with the wealth of biological knowledge for the laboratory mouse that is available from the Mouse Genome Informatics (MGI) database. energy production, biosynthesis, cell, cellular, degradation, detoxification, metabolism, mouse, physiological, enzymatic reaction, gene, disease, genome, metabolic pathway, pathway, compound, enzymatic reaction, protein, rna, reaction, blast, human, mammal, genetic, genomic is related to: Mouse Genome Informatics (MGI)
is related to: Gene Ontology
has parent organization: Jackson Laboratory
NHGRI HG003622 PMID:19682380 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10303 SCR_001791 MouseCyc database, Mouse Genome Informatics: MouseCyc database 2026-02-16 09:45:35 9

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