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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Metabolic Network Exchange Resource Report Resource Website 1+ mentions |
Metabolic Network Exchange (RRID:SCR_008124) | data or information resource, database | MetNet database contains information on networks of metabolic and regulatory and interactions in Arabidopsis. This information is based on input from biologists in their area of expertise. Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another. Other fields describing the interactions are subcellular location, confidence, directionality, references, evidence, and synonyms. Data on entities (DNA, RNA, polypeptides, protein complexes, metabolites) are derived from web databases (gene related databases: TAIR, GO, MapMan/GabiPD; protein related databases: PPDB, AMPDB, AtNoPDB, AraPerox, PLprot, BRENDA; metabolite related databases: ChEBI, PubChem, KEGG, NCI compound library, NIST MS library), in some cases with additional annotation by experts. Network information from MetNetDB can be converted to an XML file by XML Builder. From this XML file, it can be transferred to exploRase, which uses the network in conjunction with statistical analysis of expression data; to Cytoscape/FCM, which finds cycles and pathways in the network, and visualizes and models it in combination with expression data; and to MetNetVR, where the network can be visualized in 3D. | allosteric regulation, arabidopsis, interaction, metabolic, protein, regulatory, subcellular, transcription, translation | has parent organization: Iowa State University; Iowa; USA | nif-0000-20871 | SCR_008124 | MetNetDB | 2026-02-14 02:06:11 | 1 | |||||||||
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Kinase Pathway Database Resource Report Resource Website 1+ mentions |
Kinase Pathway Database (RRID:SCR_008199) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. KinasePathwayDatabase 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 47,000 and orthologous tables. | eukaryote, functional, automatic, classification, conservation, domain, interaction, intermolecular interactions and signaling pathways databases, kinase, orthologous, pathway, protein, sequence, specie, structural, image | has parent organization: University of Tokyo; Tokyo; Japan | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21235 | SCR_008199 | Kinase Pathway Database | 2026-02-14 02:06:34 | 2 | ||||||||
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The Protein Coil Library Resource Report Resource Website 1+ mentions |
The Protein Coil Library (RRID:SCR_008233) | data or information resource, database | The Protein Coil Library is a library of protein structure fragments derived from the Protein Data Bank (PDB). The fragments in this library are those fragments in the PDB that cannot be classified as either alpha-helix or beta-strand. Three-dimensional structures as well as side-chain and backbone torsion angles are stored in the database. The Protein Coil Library allows rapid and comprehensive access to non-alpha-helix and non-beta-strand fragments contained in the Protein Data Bank (PDB). The library contains both sequence and structure information together with calculated torsion angles for both the backbone and side chains. Several search options are implemented, including a query function that uses output from popular PDB-culling servers directly. Additionally, several popular searches are stored and updated for immediate access. The library is a useful tool for exploring conformational propensities, turn motifs, and a recent model of the unfolded state. The library stores the complete torsion angle descriptions for the fragments as well as the three dimensional structures of the fragments themselves. The goal of extracting and pre-calculating this data is to allow for more straightforward investigation of peptide structure without the background of secondary structure elements. In addition to searching by PDB ID, it is possible to download a particular size class, perform a batch search of PDB/chain ID''s, or download precompiled lists of PDB ID''s of interest (PDB Select, etc.). For users interested in browsing the entire database at once or maintaining their own locally-updated copy of the library, FTP access instructions are also provided. The files stored in the coil library FTP site or returned after a batch search are organized heirarchically by PDB ID. This is done to reduce filesystem access times and fascilitate searches using the UNIX find utility. At the lowest directory level in the heirarchy, files are further sorted by fragment length. As a result, the number of files in a particular directory is generally less then 50, yielding relatively fast access on UNIX/Linux filesystems. The heirarchical organization is based on the middle two letters of the PDB ID. For example, hen egg lysozyme, which has a PDB ID of 1HEL, will be located in the directory h/he/. At the final level, fragments of varying sizes are stored in directories that correspond to their fragment length. Again, using lysozyme as an example, any seven-residue fragments, if they exist, will reside in the directory h/he/7/. Similarly, seven-residue fragments from 2HEX and 1HE0 will also be in this location. Sponsors: The Protein Coil Library is funded by Johns Hopkins University. | element, fragment, alpha helix, angle, backbone, beta, coil, lysozyme, peptide, protein, protein structure databases, secondary, sequence, side chain, strand, structure, torsion | has parent organization: Johns Hopkins University; Maryland; USA | nif-0000-21338 | SCR_008233 | The Coil Library | 2026-02-14 02:06:42 | 1 | |||||||||
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Hybrid Pattern Library Resource Report Resource Website |
Hybrid Pattern Library (RRID:SCR_008193) | HyPaLib | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. It contains annotated structural elements characteristic for certain classes of structural and/or functional RNAs. These elements are described in a language specifically designed for this purpose. The language allows convenient specification of hybrid patterns, i.e. motifs consisting of sequence features and structural elements together with sequence similarity and thermodynamic constraints. A system that searches complex patterns (on nucleic-acid or protein level) in large biosequence-databases. As patterns, they allow hybrid patterns, which combine sequence similarity, structure similarity and arbitrary characteristics, like thermodynamic constraints. Applications are in the research of highly specific Protein/RNA-interactions or in the search of RNA-tertiary-structure-interactions. They developed a declarative pattern description language, which is implemented by known and new pattern-matching algorithms and an optimizing backtracking procedure. To achieve high efficiency when screening large data sets, the patterns are divided and queries are composed. The significance of patterns is estimated by a Monte-Carlo procedure. Complex results of queries are processed by a visualizing component. A library of biologically relevant patterns is developed and it is provided on the WWW together with the search-tool. The evaluation of the tool w.r.t. to the biosequence databases will in some cases mean to make laboratory-experiments, in order to check algorithmically developed functional hypothesis. Sponsors: This project is supported by a grant from the Deutsche Forschungsgemeinschaft. It is part of the special program on Computational Methods for the Analysis and Interpretation of large genomic data | element, functional, biologically, biosequence, characteristic, class, constraint, hybrid, interaction, nucleic acid, pattern, protein, rna, screening, structural, tertiary, thermodynamic | has parent organization: Bielefeld University; North Rhine-Westphalia; Germany | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21208 | SCR_008193 | Hybrid Pattern Library | 2026-02-14 02:06:12 | 0 | |||||||
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Cytokine Family Database Resource Report Resource Website 1+ mentions |
Cytokine Family Database (RRID:SCR_008134) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. A collection of cDNA, gene and protein records of cytokines deposited in public databases provides various information about the cytokine members of vertebrates in other databases including NCBI GenBank, Swiss-Prot, UniGene, TIGR (The Institute for Genomic Research) Gene Indices, Ensembl, Entrez Gene, Mouse Genome Informatics (MGI) and Rat Genome Database (RGD). It also provides orthologous relationship of cytokine members and includes novel members identified in the databases. | family, fish, gene, amphibian, bird, cdna, chemokine, cow, cytokine, genome, human, mammalian, mouse, oncogene, phylogenetic, protein, rat, receptor, reptile, virus |
is listed by: 3DVC has parent organization: Kumamoto University; Kumamoto; Japan |
Japan Society for the Promotion of Science | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20948 | http://cytokine.medic.kumamoto-u.ac.jp/ | SCR_008134 | dbCFC | 2026-02-14 02:06:12 | 1 | ||||||
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Ancient conserved untranslated sequences Resource Report Resource Website |
Ancient conserved untranslated sequences (RRID:SCR_008130) | ACUTS | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, Documented on August 12, 2014. Database that identifies new regulatory elements in untranslated regions of protein-coding genes (5 prime flanks, 5 prime UTRs, introns, 3 prime UTRs and 3 prime flanks). The analyses is focused on genes from metazoan species (essentially vertebrates, insects and nematodes). Information on highly conserved regions (sequences, alignments, annotations, bibliographic references) are compiled. Currently 176 out of 326 detected highly conserved regions (HCRs) have been analyzed and incorporated in the database. You can also access the list of annotated conserved elements and the list of conserved elements that remain to be processed. Their approach is based on comparative sequence analysis, for the identification of phylogenetic footprints. | echinoderm, footprint, fragment, functional, gene, alignment, analysis, annotation, chordate, cis-element, coding, degradation, divergence, dna, dnase, highly conserved region, homologous, intron, metazoan, mrna, non-coding, nucleotide, phylogenetic, post-transcriptional, promoter, protein, region, regulatory, segment, sequence, structural, transcriptional repressor, translation, untranslated region | has parent organization: Claude Bernard University Lyon 1; Lyon; France | PMID:9204283 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20934 | SCR_008130 | 2026-02-14 02:06:41 | 0 | |||||||
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Protein Data Bank Bind Database Resource Report Resource Website 1+ mentions |
Protein Data Bank Bind Database (RRID:SCR_008224) | PDBBIND Database | data or information resource, database | A database of binding affinities for the protein-ligand complexes in the Protein Data Bank (PDB). The PDBbind database is a collection of the experimentally measured binding affinities exclusively for the protein-ligand complexes available in the Protein Data Bank (PDB). It thus provides a link between energetic and structural information of those complexes and may be of great value to various molecular recognition studies. This site was last updated in 2007. The updated version of the resource is maintained by the Shanghai Institute of Organic Chemistry (http://www.pdbbind.org.cn). | energetic, affinity, atom, bind, bond, ligand, model, molecular, molecule, protein, structural, type |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is used by: Drug Design Data Resource |
University of Michigan; Michigan; USA ; Office of the Vice President of Research |
nif-0000-21314 | SCR_008224 | Protein DataBank Bind Database | 2026-02-14 02:06:42 | 2 | |||||||
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Protein Data Bank Site Resource Report Resource Website 1+ mentions |
Protein Data Bank Site (RRID:SCR_008227) | PDBSITE | data or information resource, database | Protein Data Bank (PDB) contains data on the spatial protein structures and their biologically active sites (i.e., ligand binding regions, enzyme catalytic centers, regions subjected to biochemical modifications, etc.). However, neither of the well known systems searching PDB does not provide the user with possibility to make the queries related with the active sites. A database PDBSITE storing the data on biologically active sites contained in the PDB database has been developed. PDBSITE accumulates amino acid content, structure features calculated by spatial protein structures, and physicochemical properties of sites and their spatial surroundings. | enzyme, functional, active, activity, amino acid, binding, biochemical, biological, biologically, biology, biotechnology, catalytic, dna, heterocomplex, inorganic, interaction, ligand, medicine, modification, molecular, organic, pattern, physiochemical, post-translational, primary, protein, protein sequence motifs and active sites databases, residue, rna, site, spatial, specificity, structural, structure, tertiary |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is used by: PASSer has parent organization: Siberian Branch of the Russian Academy of Sciences; Novosibirsk; Russia |
PMID:15608173 | nif-0000-21317 | SCR_008227 | 2026-02-14 02:06:08 | 1 | ||||||||
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Phylogenetic Clusters of Orthologous Groups Ranking Resource Report Resource Website 1+ mentions |
Phylogenetic Clusters of Orthologous Groups Ranking (RRID:SCR_008223) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 20,2019.The COG-database has become a powerful tool in the field of comparative genomics. The construction of this data-base is based on sequence homologies of proteins from different completely sequenced genomes. Highly homologous proteins are assigned to clusters of orthologous groups. The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for functional annotation of newly sequenced genomes, including those of complex eukaryotes, and genome-wide evolutionary studies. The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. Here is a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted) proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs) include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens), one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe), and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or approximately 54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of approximately 20% of the KOG set. This conserved portion of the KOG set is much greater than the ubiquitous portion of the COG set (approximately 1% of the COGs). In part, this difference is probably due to the small number of included eukaryotic genomes, but it could also reflect the relative compactness of eukaryotes as a clade and the greater evolutionary stability of eukaryotic genomes. | elegans, encephalitozoon, eukaryote, evolutionary, fly, fruit, fungus, gene, general genomics databases, animal, arabidopsis, caenorhabditis, cerevisiae, classification, comparative, cuniculi, drosophila, genome, genomic, homo, homology, intracellular, melanogaster, microsporidian, nematode, organism, ortholog, orthologous, parasite, pattern, phyletic, phylogenetic, plant, pombe, prokaryote, protein, saccharomyces, sapiens, schizosaccharomyces, sequence, thaliana, tool, unicellular | has parent organization: National Institutes of Health | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21313 | SCR_008223 | PCOGR | 2026-02-14 02:06:13 | 3 | ||||||||
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LPDB: Ligand-Protein DataBase Resource Report Resource Website 1+ mentions |
LPDB: Ligand-Protein DataBase (RRID:SCR_008172) | data or information resource, database | The Ligand Protein Database is designed to allow the selection of complexes based on various properties of receptors and ligands for the design and parametrization of new scoring functions or to assess and improve existing ones. Moreover, for each complex, a continuum of ligand positions ranging from the crystallographic position to points on the surface of the protein receptor allows an assessment of the energetic behavior of particular scoring functions. Access to the database is password protected. To obtain access to the LPDB, complete a form, available online, have it signed by your research advisor, and fax the completed form back to the attention of Professor Charles L. Brooks III, (858) 784-8688. There is no fee for academic use of the LPDB. We are currently working out details for licensing to our colleagues in industry. Please contact Professor Brooks to obtain current information on access to the LPDB. | complexes, ligand, protein, receptors | has parent organization: University of Michigan; Ann Arbor; USA | nif-0000-21245 | SCR_008172 | LPDB | 2026-02-14 02:06:07 | 2 | |||||||||
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Peroxisome Database Resource Report Resource Website 10+ mentions |
Peroxisome Database (RRID:SCR_008352) | data or information resource, database | The aim of the PEROXISOME database (PeroxisomeDB) is to gather, organize and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders. PeroxisomeDB contains the complete peroxisomal proteome of Homo sapiens (encoded by 85 genes) and Saccharomyces cerevisiae (encoded by 61 genes). Now, we have included 34 new organism genomes with the acquisition of 2426 new peroxisomal homolog proteins. PeroxisomeDB 2.0 integrates the peroxisomal metabolome of whole microbody family by the new incorporation of the glycosome proteomes of trypanosomatids and the glyoxysome proteome of Arabidopsis thaliana. The site also provides a Peroxisome Metabolome of peroxisomal genes and proteins, their molecular interactions and metabolic pathways, tools for comparative genomics, predictive tools. Sponsors: Preoxisome Database is funded by Institut de Gntique et deBiologie Molculaire et Cellulaire. | family, function, gene, arabidopsis thaliana, disorder, genome, genomic, glycosome, glyoxysome, homolog, homo sapiens, interaction, metabolic, metabolome, microbody, molecular, organism, pathway, peroxisome, protein, proteome, saccharomyces cerevisiae, trypanosomatid | nif-0000-25216 | SCR_008352 | Preoxisomedb | 2026-02-14 02:06:35 | 27 | ||||||||||
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Structure modeling of 907 G protein coupled receptors in the human genome Resource Report Resource Website 1+ mentions |
Structure modeling of 907 G protein coupled receptors in the human genome (RRID:SCR_008351) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19,2019.Database of tertiary structural modeling results of threading assembly refinement (TASSER) method for all 907 G protein-coupled receptors (GPCRs) in human genome. All sequences were collected from GPCR database http://www.gpcr.org/7tm/ and http://www.expasy.org/cgi-bin/lists?7tmrlist.txt. Unlike traditional homology modeling approaches, TASSER modeling does not require solved homologous template structures; moreover, it often refines the structures closer to native. G protein-coupled receptors (GPCRs), encoded by about 5% of human genes, comprise the largest family of integral membrane proteins and act as cell surface receptors responsible for the transduction of endogenous signal into a cellular response. Although tertiary structural information is crucial for function annotation and drug design, there are few experimentally determined GPCR structures. To address this issue, we employ the recently developed threading assembly refinement (TASSER) method to generate structure predictions for all 907 putative GPCRs in the human genome. Unlike traditional homology modeling approaches, TASSER modeling does not require solved homologous template structures; moreover, it often refines the structures closer to native. These features are essential for the comprehensive modeling of all human GPCRs when close homologous templates are absent. Based on a benchmarked confidence score, approximately 820 predicted models should have the correct folds. The majority of GPCR models share the characteristic seven-transmembrane helix topology, but 45 ORFs are predicted to have different structures. This is due to GPCR fragments that are predominantly from extracellular or intracellular domains as well as database annotation errors. Our preliminary validation includes the automated modeling of bovine rhodopsin, the only solved GPCR in the Protein Data Bank. With homologous templates excluded, the final model built by TASSER has a global C(alpha) root-mean-squared deviation from native of 4.6 angstroms, with a root-mean-squared deviation in the transmembrane helix region of 2.1 angstroms. Models of several representative GPCRs are compared with mutagenesis and affinity labeling data, and consistent agreement is demonstrated. Structure clustering of the predicted models shows that GPCRs with similar structures tend to belong to a similar functional class even when their sequences are diverse. These results demonstrate the usefulness and robustness of the in silico models for GPCR functional analysis. Sponsors: GPCR is funded by the University at Buffalo, Buffalo, New York. | endogenous, extracellular, family, functional, gene, cellular, couple, genome, gpcr, g protein, helix, homology, human, membrane, model, modeling, orf, protein, receptor, response, signal, structural, structural model, structure, template, tertiary, topology, transduction, transmembrane | has parent organization: Georgia Institute of Technology; Georgia; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25215 | SCR_008351 | GPCR | 2026-02-14 02:06:08 | 3 | ||||||||
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MitoInteractome Resource Report Resource Website |
MitoInteractome (RRID:SCR_010225) | MitoInteractome | data or information resource, database | Database that gathers data on interactions in the mitochondrial proteome that has been used to construct a network for the aging process in humans and to identify interactions that influence this process, since mitochondria is a major source of cellular reactive oxygen species that accumulate during aging. It will: # aid in increasing our understanding of the molecular functions and interaction networks of mitochondrial proteins, # help in identifying new target proteins for experimental research using predicted protein-protein interaction information, and # help in identifying biomarkers for diagnosis and new molecular targets for drug development related to mitochondria. How is MitoInteractome different? * Provides protein-protein interaction information with graphical display. * Applies newly added new mitochondrial protein information by using BLAST incorporated in Mitointeractome * Shows correlation of mutation with their impact * Provides specific pathway information to aid study of their impact * Contains SNP Information | interaction, mitochondrial proteome, mitochondria, protein-protein interaction, physico-chemical property, polymorphism, protein sequence, protein, disease, snp, pathway | has parent organization: Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea | Aging | PMID:19958484 | nlx_156772 | SCR_010225 | MitoInteractome - Mitochondrial Protein Interactome Database | 2026-02-14 02:06:11 | 0 | ||||||
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UniPathway Resource Report Resource Website 10+ mentions |
UniPathway (RRID:SCR_010513) | UniPathway | data or information resource, database | A manually curated database of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. Users may do a quick search, browse pathway, browse compound, or browse organism. | metabolic pathway, pathway annotation, pathway, annotation, chemical reaction, protein, compound |
is related to: UniProtKB has parent organization: PrabiG has parent organization: SIB Swiss Institute of Bioinformatics |
Swiss Federal Government ; GIS-IBISA ; European Union SISYPHE ; European Union SLING 226073; European Union Microme 222886-2; French Government ANR MIRI BLAN08-1335497 |
PMID:22102589 | nlx_16723 | SCR_010513 | UniPathway: a metabolic door to UniProtKB/Swiss-Prot, UniPathway: a resource for the exploration of metabolic pathways | 2026-02-14 02:06:37 | 17 | ||||||
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Mouse Genome Database Resource Report Resource Website 500+ mentions |
Mouse Genome Database (RRID:SCR_012953) | MGD | data or information resource, database | Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. | gene, genome, genetic, chromosome, clone, cytogenetic, dna, genomic, inbred, mammalian, mouse, mutant, ortholog, phenotype, primer, protein, reagent, sequence, strain, bio.tools |
is used by: DisGeNET is listed by: Debian is listed by: bio.tools is related to: Mouse Genome Informatics (MGI) has parent organization: Jackson Laboratory |
NHGRI HG000330 | PMID:21051359 | biotools:mgi, biotools:mgd, nif-0000-10301 | http://www.informatics.jax.org/mgihome/projects/overview.shtml https://bio.tools/mgd https://bio.tools/mgi |
SCR_012953 | Mouse Genome Informatics: Mouse Genome Database, MGID, Mouse Genome Informatics Database | 2026-02-14 02:06:41 | 502 | |||||
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Antibodypedia Resource Report Resource Website 10+ mentions |
Antibodypedia (RRID:SCR_012782) | data or information resource, database | Open-access database of antibodies against human proteins developed through collaboration between Antibodypedia AB and the Nature Publishing Group. It aims to provide the scientific community and antibody distributors alike with information on the effectiveness of specific antibodies in specific applications--to help scientists select the right antibody for the right application. Antibodypedia's mission is to promote the functional understanding of the human proteome and expedite analysis of potential biomarkers discovered through clinical efforts. To this end, they have developed an open-access, curated, searchable database containing annotated and scored affinity reagents to aid users in selecting antibodies tailored to specific biological and biomedical assays. They envisage Antibodypedia as a virtual repository of validated antibodies against all human, and ultimately most model-organism, proteins. Such a tool will be exploitable to identify affinity reagents to document protein expression patterns in normal and pathological states and to purify proteins alone and in complex for structural and functional analyses. They hope to promote characterization of the roles and interplay of proteins and complexes in human health and disease. They encourage commercial providers to submit information regarding their inventory of antibodies with links to quality control data. Independent users can submit their own application-specific experimental data using standard validation criteria (supportive or non-supportive) developed with the assistance of an international advisory board recruited from academic research institutions. Users can also comment on specific antibodies without submitting validation data. | cell biology, antibody, protein, human, reagent, model organism, non-human primate, FASEB list |
is listed by: 3DVC is listed by: OMICtools is related to: Nature Publishing Group |
Antibodypedia AB ; Nature Publishing Group ; European Union 6th framework - ProteomeBinders ; Human Antibody Initiative ; HUPO - Human Proteome Organisation |
PMID:18667413 PMID:18767878 |
The community can contribute to this resource | nif-0000-22918, OMICS_01770 | SCR_012782 | Antibodypedia / Nature | 2026-02-14 02:06:16 | 44 | ||||||
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SYFPEITHI: A Database for MHC Ligands and Peptide Motifs Resource Report Resource Website 100+ mentions |
SYFPEITHI: A Database for MHC Ligands and Peptide Motifs (RRID:SCR_013182) | SYFPEITHI | data or information resource, database | SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only. It contains a collection of MHC class I and class II ligands and peptide motifs of humans and other species, such as apes, cattle, chicken, and mouse, for example, and is continuously updated. Searches for MHC alleles, MHC motifs, natural ligands, T-cell epitopes, source proteins/organisms and references are possible. Hyperlinks to the EMBL and PubMed databases are included. In addition, ligand predictions are available for a number of MHC allelic products. The database is based on previous publications on T-cell epitopes and MHC ligands. It contains information on: -Peptide sequences -anchor positions -MHC specificity -source proteins, source organisms -publication references Since the number of motifs continuously increases, it was necessary to set up a database which facilitates the search for peptides and allows the prediction of T-cell epitopes. The prediction is based on published motifs (pool sequencing, natural ligands) and takes into consideration the amino acids in the anchor and auxiliary anchor positions, as well as other frequent amino acids. The score is calculated according to the following rules: The amino acids of a certain peptide are given a specific value depending on whether they are anchor, auxiliary anchor or preferred residue. Ideal anchors will be given 10 points, unusual anchors 6-8 points, auxiliary anchors 4-6 and preferred residues 1-4 points. Amino acids that are regarded as having a negative effect on the binding ability are given values between -1 and -3. Sponsors: SYFPEITHI is supported by DFG-Sonderforschungsbereich 685 and theEuropean Union: EU BIOMED CT95-1627, BIOTECH CT95-0263, and EU QLQ-CT-1999-00713. | epitope, allele, allelic, amino acid, ape, bind, cattle, chicken, class i, class ii, human, immunological database, ligand, mhc, molecule, motif, mouse, natural, organism, peptide, product, protein, sequence, specie, t-cell, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Tubingen; Tubingen; Germany |
nif-0000-21383, biotools:syfpeithi | https://bio.tools/syfpeithi | SCR_013182 | SYFPEITHI | 2026-02-14 02:06:48 | 258 | |||||||
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Cube-DB Resource Report Resource Website 1+ mentions |
Cube-DB (RRID:SCR_013233) | Cube-DB | data or information resource, database | Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family classification follows (largely) the classification suggested by HUGO Gene Nomenclature Committee. Sets of orhtologous protein sequences were generated by mutual-best-hit strategy using full vertebrate genomes available in Ensembl. The scores, described on documentation page, are assigned to each individual residue in a protein, and presented in the form of a table (html or downloadable xls formats) and mapped, when appropriate, onto the related structure (Jmol, Pymol, Chimera). | protein, functional divergence, vertebrate, genome, ortholog, protein sequence, data set, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Bioinformatics Institute; Singapore; Singapore |
PMID:22139934 | nlx_149432, biotools:cube-db | https://bio.tools/cube-db | SCR_013233 | Cube-DB: Detection of Functional Divergence in Human Protein Families | 2026-02-14 02:06:17 | 3 | ||||||
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Alzforum Antibody Directory for Neuroscience Research Resource Report Resource Website |
Alzforum Antibody Directory for Neuroscience Research (RRID:SCR_013601) | data or information resource, database | The Alzheimer Research Forum is the web''s most dynamic scientific community dedicated to understanding Alzheimer''s disease and related disorders. It also contains a database of providers of antibodies directed against several hundred molecules and proteins of relevant to research on Alzheimer and other neurodegenerative diseases. The web site reports on the latest scientific findings, from basic research to clinical trials; creates and maintains public databases of essential research data and reagents, and produces discussion forums to promote debate, speed the dissemination of new ideas, and break down barriers across the numerous disciplines that can contribute to the global effort to cure Alzheimer''s disease. The ARF team of professional science writers and editors, information technology experts, web developers and producers all work closely with our distinguished and diverse Advisory Board to ensure a high-quality of information and services. We very much welcome our readers'' participation in all aspects of the web site. Sponsors: The Alzheimer Research Forum is an independent nonprofit organization. It is supported by grants and individual donations. | alzheimer, antibody, clinical trail, community, data, disease, disorder, molecule, neurodegenerative, protein, reagent, research, science, scientific, technology | has parent organization: Alzheimer's Research Forum | nif-0000-00129 | SCR_013601 | Alzforum Antibody Directory | 2026-02-14 02:06:26 | 0 | |||||||||
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iPTMnet Resource Report Resource Website 10+ mentions |
iPTMnet (RRID:SCR_014416) | data or information resource, database | A protein database which connects multiple disparate bioinformatics tools and systems text mining, data mining, analysis and visualization tools, and databases and ontologies. | database, protein, phosphorylation, bioinformatics, text mining, ontology | NSF ABI-1062520 | Available to the research community | SCR_014416 | 2026-02-14 02:06:28 | 30 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
