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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.

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
PfamResource, data or information resource, databaseA database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Users can analyze protein sequences for Pfam matches, view Pfam family annotation and alignments, see groups of related families, look at the domain organization of a protein sequence, find the domains on a PDB structure, and query Pfam by keywords. There are two components to Pfam: Pfam-A and Pfam-B. Pfam-A entries are high quality, manually curated families that may automatically generate a supplement using the ADDA database. These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found. Pfam also generates higher-level groupings of related families, known as clans (collections of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM).database, clan, structure, sequence, protein family, domainSCR_004726(Pfam, RRID:SCR_004726)Wellcome Trust Sanger Institute; Hinxton; United Kingdom BBSRC, EMBL core funds, Howard Hughes Medical Institute, Wellcome Trustrelated to: Conserved Domain Database, Monarch Initiative, SUPFAM, DBD: Transcription factor prediction database, DOMINE: Database of Protein Interactions, GeneSpeed- A Database of Unigene Domain Organization , Eukaryotic Linear Motif, TopoSNP, GOTaxExplorer, TrED, ProOpDB, Algal Functional Annotation Tool, used by: Mutation Annotation and Genomic Interpretation, MobiDB, listed by: OMICtoolsReferences (2)Last checked downnlx_72111, OMICS_01696http://pfam.sanger.ac.uk/
CoCoMacResource, data or information resource, databaseOnline access (html or xml) to structural connectivity ("wiring") data on the Macaque brain. The database has become by far the largest of its kind, with data extracted from more than four hundred published tracing studies. The main database, contains data from tracing studies on anatomical connectivity in the macaque cerebral cortex. Also available are a variety of tools including a graphical simulation workbench, map displays and the CoCoMac-Paxinos-3D viewer. Submissions are welcome. To overcome the problem of divergent brain maps ORT (Objective Relational Transformation) was developed, an algorithmic method to convert data in a coordinate- independent way based on logical relations between areas in different brain maps. CoCoMac data is used to analyze the organization of the cerebral cortex, and to establish its structure- function relationships. This includes multi-variate statistics and computer simulation of models that take into account the real anatomy of the primate cerebral cortex. This site * Provides full, scriptable open access to the data in CoCoMac (you must adhere to the citation policy) * Powers the graphical interface to CoCoMac provided by the Scalable Brain Atlas * Sports an extensive search/browse wizard, which automatically constructs complex search queries and lets you further explore the database from the results page. * Allows you to get your hands dirty, by using the custom SQL query service. * Displays connectivity data in tabular form, through the axonal projections service. CoCoMac 2 was initiated at the Donders Institute for Brain, Cognition and Behaviour, and is currently supported by the German neuroinformatics node and the Computational and Systems Neuroscience group at the Juelich research institute.brain, macaque, non-human primate, connectivity, microcircuitry, prefrontal cortex, neural network, structure, function, neuroanatomy, brain circuitry, axonal projection, data repository, visualization, atlas application, computational neuroscience, magnetic resonance, ontology, php, tractography, web environment, softwareSCR_007277(CoCoMac, RRID:SCR_007277)German Neuroinformatics Node DFG, Heinrich-Heine University of Dusseldorf; Dusseldorf; Germany, Wellcome Trustrelated to: Scalable Brain Atlas, used by: NIF Data Federation, Integrated Nervous System Connectivity, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)References (5)Last checked downnif-0000-00022http://www.nitrc.org/projects/cocomac, http://134.95.56.239/home.asphttp://cocomac.org/, http://cocomac.g-node.org/drupal/
RfamResource, data analysis service, database, analysis service resource, production service resource, service resource, data or information resourceThe Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: Non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. Rfam is also available via FTP. You can find data in Rfam in various ways... * Analyze your RNA sequence for Rfam matches * View Rfam family annotation and alignments * View Rfam clan details * Query Rfam by keywords * Fetch families or sequences by NCBI taxonomy * Enter any type of accession or ID to jump to the page for a Rfam family, sequence or genomefamily, genome, clan, structure, non-coding rnaSCR_007891(Rfam, RRID:SCR_007891)Wellcome Trust Sanger Institute; Hinxton; United Kingdom Howard Hughes Medical Institute, University of Manchester; Manchester; United Kingdom, Wellcome TrustPMID:21062808Last checked downnif-0000-03402http://rfam.sanger.ac.uk/
Potassium Channel DatabaseResource, data set, data or information resourceA Database of Potassium Ion Channel Homology Models & Molecular Dynamics Simulations.potassium ion channel, homology model, crystal structure, molecular dynamics, simulation, structure, imageSCR_011960(Potassium Channel Database, RRID:SCR_011960)University of Oxford; Oxford; United Kingdom BBSRC, Wellcome Trustlisted by: OMICtoolsLast checked upOMICS_01609
JpredResource, data analysis software, data processing software, software application, sequence analysis software, data analytics software, software resourceSoftware tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions.protein, secondary, structure, prediction, amino, acid, sequence, accurate, JNet algorithm, solvent, accessibility, coiled, coil, regionSCR_016504(Jpred, RRID:SCR_016504)Biotechnology and Biological Sciences Research Council, Wellcome TrustDOI:10.1093/nar/gkn238Last checked up
SGCResourceA not-for-profit, public-private partnership that carries out basic science of relevance to drug discovery whose core mandate is to determine 3D structures on a large scale and cost-effectively - targeting human proteins of biomedical importance and proteins from human parasites that represent potential drug targets.basic science, drug discovery, drug, structural genomics, genomics, 3d structure, protein, human parasite, drug target, structure, human protein, protocol, phylogenetic tree, histone tail, high-throughput protein crystallization, lex bubbling system, reagent, epigenetic probe, antibody, vector, plasmid, constructSCR_003890(SGC, RRID:SCR_003890)University of Oxford; Oxford; United Kingdom , University of Toronto; Ontario; Canada Cancer, Diabetes, Obesity, Psychiatric disorderAbbVie, Boehringer Ingelheim, Canada Foundation for Innovation, Canadian Institutes of Health Research, Genome Canada, GlaxoSmithKline, Janssen, Lilly Canada, Novartis Research Foundation, Ontario Ministry of Economic Development Employment and Infrastructure, Pfizer, Takeda, Wellcome Trustrelated to: AbbVie, Canada Foundation for Innovation, Canadian Institutes of Health Research, Genome Canada, Janssen Research and Development, Ontario Ministry of Economic Development Employment and Infrastructure, Pfizer Animal Genetics, Wellcome Trust, uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank, Addgene, GenBankLast checked upnlx_158220
3DSwapResource, data or information resource, databaseCurated knowledegbase of protein structures that are reported to be involved in 3-dimensional domain swapping. 3DSwap provides literature curated information and structure related information about 3D domain swapping in proteins. Information about swapping, hinge region, swapped region, extent of swapping, etc. are extracted from original research publications after extensive literature curation.protein structure, protein, structure, 3d domain swapping, function, sequence, domain swap, 3d spatial imageSCR_004133(3DSwap, RRID:SCR_004133)Tata Institute of Fundamental Research; Mumbai; India National Centre for Biological Sciences, Tata Institute of Fundamental Research; Mumbai; India, Wellcome TrustReferences (2)Last checked upnlx_143564
PDBe - Protein Data Bank in EuropeResource, service resource, data or information resource, data repository, storage service resource, databaseThe European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules.x-ray, nmr, cryo-em, hybrid method, dna, protein, rna, sugar, ligand, virus, compound, fold, enzyme, 3d spatial image, structure, macromolecule, protein-protein interaction, gold standardSCR_004312(PDBe - Protein Data Bank in Europe, RRID:SCR_004312)European Bioinformatics Institute BBSRC, CCP4, European Molecular Biology Laboratory; Heidelberg; Germany, European Union, MRC, NIH, Wellcome Trustrelated to: Research Collaboratory for Structural Bioinformatics Protein Data Bank, DDBJ - DNA Data Bank of Japan, EMDataBank.org: Unified Data Resource for Cryo Electron Microscopy, Worldwide Protein Data Bank , Biological Magnetic Resonance Data Bank, DDBJ - DNA Data Bank of Japan, Worldwide Protein Data Bank , PDBj - Protein Data Bank Japan, Research Collaboratory for Structural Bioinformatics Protein Data Bank, RCSB PDB, listed by: re3data.orgReferences (3)Last checked upnlx_32372
FunTreeResource, data or information resource, databaseFunTree provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH. To access the resource enter a specific CATH superfamily code or search for a structure / sequence / function (either via a EC code or KEGG ligand / reaction ID, PDB ID or UniProtKB ID). Or browse the resource via superfamily / function / structure / metabolites & reactions via the menu on the left panel. FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme''''s sequence and structure but also the relationships of their reactions. Developed in tandem with the CATH database, it currently comprises 276 superfamilies covering 1800 (70%) of sequence assigned enzyme reactions. Central to the resource are phylogenetic trees generated from structurally informed multiple sequence alignments using both domain structural alignments supplemented with domain sequences and whole sequence alignments based on commonality of multi-domain architectures. These trees are decorated with functional annotations such as metabolite similarity as well as annotations from manually curated resources such the catalytic site atlas and MACiE for enzyme mechanisms.enzyme function, enzyme superfamily, enzyme, sequence, structure, phylogenetic, chemical, mechanistic, functional annotation, superfamily, gold standardSCR_006014(FunTree, RRID:SCR_006014)European Bioinformatics Institute BBSRC, DOE, European Molecular Biology Laboratory; Heidelberg; Germany, Wellcome Trustrelated to: CATH: Protein Structure Classification, Research Collaboratory for Structural Bioinformatics Protein Data Bank, KEGG, UniProtKBPMID:22006843Last checked upnlx_151402
PDBsumResource, data analysis service, production service resource, analysis service resource, database, service resource, d spatial image, data or information resourcePictorial database of an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of their interactions. Extensive use is made of the freely available RasMol molecular graphics program to view the molecules and their interactions in 3D. Entries are accessed either by their 4-character PDB code, or by one of the two search boxes provided on the PDBsum home page: text search or sequence search. The information given on each PDBsum entry is spread across several pages, as listed below and accessible from the tabs at the top of the page. Only the relevant tabs will be present on any given page. * Top page - summary information including thumbnail image of structure, molecules in structure, enzyme reaction diagram (where relevant), GO functional assignments, and selected figures from key reference * Protein - wiring diagram, topology diagram(s) by CATH domain, and residue conservation (where available) * DNA/RNA - DNA/RNA sequence and NUCPLOT showing interactions made with protein * Ligands - description of bound molecule and LIGPLOT showing interactions made with protein * Prot-prot - schematic diagrams of any protein-protein interfaces and the residue-residue interactions made across them * Clefts - listing of top ten clefts in the surface of the protein, listed by volume with any bound ligands shown * Links - links to external databases Additionally, it accepts users'''' own PDB format files and generates a private set of analyses for each uploaded structure.3d structure, protein, molecule, structure, protein chain, dna, ligand, metal ion, interaction, gold standardSCR_006511(PDBsum, RRID:SCR_006511)European Bioinformatics Institute Wellcome Trustrelated to: ProFunc, SAS - Sequence Annotated by Structure, ArchSchema, Research Collaboratory for Structural Bioinformatics Protein Data Bank, DrugPort, Enzyme Structures DatabaseReferences (4)Last checked upnlx_40623
Worldwide Protein Data Bank Resource, data or information resource, resource, databaseA free and public single global PDB archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.3-dimentional, bioinformatics, protein, research, structure, macromolecule, structural data, 3d spatial image, gold standardSCR_006555( Worldwide Protein Data Bank , RRID:SCR_006555)BBSRC, DOE, European Molecular Biology Laboratory; Heidelberg; Germany, European Union, Japan Science and Technology Agency, NBDC - National Bioscience Database Center, NCI, NIDDK, NIGMS, NIH, NINDS, NLM, NSF, Wellcome Trustrelated to: Biological Magnetic Resonance Data Bank, Proteopedia - Life in 3D, NRG-CING, Research Collaboratory for Structural Bioinformatics Protein Data Bank, DDBJ - DNA Data Bank of Japan, PDBe - Protein Data Bank in Europe, PDBe - Protein Data Bank in Europe, PDBj - Protein Data Bank Japan, Biological Magnetic Resonance Data Bank, Research Collaboratory for Structural Bioinformatics Protein Data Bank, used by: Ligand ExpoPMID:14634627Last checked upnif-0000-23903
Enzyme Structures DatabaseResource, data or information resource, image collection, databaseDatabase of known enzyme structures that have been deposited in the Protein Data Bank (PDB). The enzyme structures are classified by their E.C. number of the ENZYME Data Bank. Browse the classification hierarchy or enter an EC number or search-string. There are currently 45,638 PDB-enzyme entries in the PDB (as at 23 February, 2013) involving 38,109 separate PDB files - some files having more than one E.C. number associated with them.enzyme, structure, gold standardSCR_007125(Enzyme Structures Database, RRID:SCR_007125)European Bioinformatics Institute Wellcome Trustrelated to: PDBsum, Research Collaboratory for Structural Bioinformatics Protein Data BankLast checked upnlx_30980
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