> > Databases

Databases

This section contains databases of protein sequences, properties, targeting, motifs, domains, structures, and protein families.

RSS FeedCompact ViewList as XMLList as JSON

Found 115 links

Displaying 15 links

3D-FootprintDatabase Content

http://floresta.eead.csic.es/3dfootprint

DNA > Databases
Protein > Databases

3D-footprint provides estimates of binding specificity for all protein-DNA complexes available at the Protein Data Bank. The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface residues in the resulting alignments. Comparisons with expert-curated databases RegulonDB and TRANSFAC support the quality of structure-based estimates of specificity.

This content is being maintained by brunocontreras.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals bacterial proteins computational biology dna-binding proteins genetic databases genetic regulation humans nucleic acid databases protein conformation protein databases protein-DNA complex pubmed regulator genes sequence alignment

3didDatabase Content

http://3did.irbbarcelona.org/

Protein > Databases

The database of three-dimensional interacting domains (3did) is a collection of protein interactions for which high-resolution three-dimensional structures are known. The interface residues are presented for each interaction type individually, plus global domain interfaces at which one or more partners (domains or peptides) bind. The 3did web server visualizes these interfaces along with atomic details of individual interactions using Jmol.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsmolecular models peptides protein databases protein interaction domains and motifs protein interaction mapping

ArachnoServer 2.0Database Content

http://www.arachnoserver.org

Model Organisms > Databases
Protein > Databases

ArachnoServer is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. Key features of ArachnoServer include a molecular target ontology designed specifically for venom toxins, current and historic taxonomic information and a powerful advanced search interface.

This content is being maintained by glennfking.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals protein databases proteins sequence analysis spider venoms spiders

ASDDatabase Content

http://mdl.shsmu.edu.cn/ASD/

Protein > Databases

AlloSteric Database (ASD) provides a central resource for the display, search and analysis of structure, function and related annotation for allosteric molecules. Proteins are annotated with a detailed description of allostery, biological process and related diseases, and modulators with binding affinity, physicochemical properties and therapeutic area.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsallosteric regulation allosteric site drug design protein databases proteins

ASPicDBDatabase Content

http://www.caspur.it/ASPicDB/

Human Genome > Databases
Protein > Databases

ASPicDB provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256,939 protein variants from 17,191 multi-exon genes have been extensively annotated through machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user.

This content is being maintained by Graziano Pesole.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalternative splicing exons genetic databases genetic variation humans messenger rna protein isoforms protein sequence analysis proteins

AtPIDDatabase Content

http://www.megabionet.org/atpid/

Model Organisms > Databases
Protein > Databases

The AtPID (Arabidopsis thaliana Protein Interactome Database) represents a centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsarabidopsis proteins molecular sequence annotation protein databases protein interaction mapping proteomics

BioSystemsDatabase Content

http://www.ncbi.nlm.nih.gov/biosystems

Protein > Databases

The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals cell membrane computational biology genes genetic databases genomics humans national library of medicine (u.s.) nucleic acid databases protein databases systems biology united states
setsNational Center for Biotechnology Information (NCBI)

BISCDatabase Content

http://bisc.cse.ucsc.edu

Protein > Databases

Binary subcomplexes in proteins database (BISC) is a protein-protein interaction (PPI) database linking up the two communities most active in their characterization: structural biology and functional genomics researchers. The BISC resource offers users (i) a structural perspective and related information about binary subcomplexes (i.e. physical direct interactions between proteins) that are either structurally characterized or modellable entries in the main functional genomics PPI databases BioGRID, IntAct and HPRD; (ii) selected web services to further investigate the validity of postulated PPI by inspection of their hypothetical modelled interfaces.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsgenetic databases genomics molecular models multiprotein complexes protein databases protein interaction mapping

BRENDADatabase Content

http://www.brenda-enzymes.org

Protein > Databases

The BRENDA (BRaunschweig ENzyme Database) enzyme information system is a collection of enzyme functional and property data, manually extracted from the primary literature. The content covers information on function, structure, occurrence, preparation and application of enzymes as well as properties of mutants and engineered variants. New query, analysis and data management tools were implemented to improve data processing, data presentation, data input and data access. BRENDA now provides new viewing options such as the display of the statistics of functional parameters and the 3D view of protein sequence and structure features. A ligand summary shows comprehensive information on the BRENDA ligands. The enzymes are linked to their respective pathways and can be viewed in pathway maps.

This content is being maintained by Dietmar Schomburg.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsenzymes ligands metabolic networks and pathways protein conformation protein databases

BriXDatabase Content

http://brix.crg.es

Protein > Databases

BriX is a vast database of protein fragments, clustered on their backbone similarity. BriX contains fragments from 7290 proteins from the Astral40 set, fragmented in lengths ranging from 4 to 14 amino acids and clustered against 6 different distance thresholds on similarity of the protein backbone. Loop BriX contains loop fragments from 14.525 proteins from the Astral95 set, clustered according to end-to-distance and anchor residue superposition.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsmolecular models protein conformation protein databases proteins

BSDBDatabase Content

http://www.ifpan.edu.pl/BSDB/

Protein > Databases

The Biomolecule Stretching Data provides information about mechanostability of proteins. Its core is based on simulations of stretching of proteins within a structure-based model. The primary information is about the heights of the maximal force peaks, the force-displacement patterns, and the sequencing of the contact-rupturing events. Information on the possible types of the mechanical clamps (the motifs which are responsible for a protein's resistance to stretching) are also given.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsbiomechanics chemical models molecular dynamics simulation protein databases proteins secondary protein structure

CATHDatabase Content

http://www.cathdb.info/

Protein > Databases

CATH is a manually curated classification of protein domain structures. Each protein has been chopped into structural domains and assigned into homologous superfamilies (groups of domains that are related by evolution). This classification procedure uses a combination of automated and manual techniques which include computational algorithms, empirical and statistical evidence, literature review and expert analysis.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsphylogeny protein databases protein folding proteins tertiary protein structure

CDDDatabase Content

http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

Protein > Databases

NCBI's Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamino acid sequence biological models conserved sequence protein databases protein sequence analysis proteins tertiary protein structure

CDDBDatabase Content

http://www.cdyn.org

Protein > Databases

The conformational dynamics data bank (CDDB) is a database for comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a coarse-grained computational approach that is applied to the majority of structures present in the electron microscopy data bank (EMDB). Results include equilibrium thermal fluctuations and elastic strain energy distributions that identify rigid versus flexible protein domains generally, as well as those associated with specific functional transitions, and correlations in molecular motions that identify molecular regions that are highly coupled dynamically. The data bank is maintained and updated automatically to include conformational dynamics results for new structural entries as they become available in the EMDB.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsmultiprotein complexes protein conformation protein databases proteins

ComSinDatabase Content

http://antares.protres.ru/comsin/.

Protein > Databases

ComSin is a database of protein structures in bound (complex) and unbound (single) states. The developed server enables one to search for proteins in bound and unbound states with several options including sequence similarity between the corresponding proteins in bound and unbound states, and validation of interaction interfaces of protein complexes.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals bacterial proteins computational biology genetic databases humans molecular conformation molecular models protein binding protein conformation protein databases tertiary protein structure

Tags associated with subcategory 'Protein/Databases'

protein databases humans animals genetic databases computational biology tertiary protein structure proteins nucleic acid databases protein interaction mapping archaeal genome signal transduction microbiology automation terminology as topic genome bacteria plant genome archaeal proteins environmental biodegradation x-ray crystallography natural language processing biological models environmental pollutants ligands catalytic domain molecular models molecular conformation protein binding controlled vocabulary gene functional similarity disease computer simulation markov chains online systems peptides chemical dictionaries antigen receptors dna sequence analysis major histocompatibility complex immunoglobulins systems biology biotransformation rna neoplastic gene expression regulation false positive reactions pharmaceutical preparations programming languages preclinical drug evaluation neoplasms human genome metabolome species specificity metabolomics peroxisomal disorders mass spectrometry ions peroxisomes protein-tyrosine kinases viral proteins saccharomyces cerevisiae multiprotein complexes genes National Center for Biotechnology Information (NCBI) biochemistry gene database national library of medicine (u.s.) mice University of Toronto fluorescent dyes antitumor drug screening assays gene library tumor cell line genetic models fungal proteins fungal genome protein database gene ontology phenotype micrornas transcription factors dna-binding proteins protein conformation genetic regulation gene regulatory networks proteomics chromatin algorithms chromatin immunoprecipitation dna methylation proteome protein isoforms histones protein-DNA complex pubmed united states sequence analysis sequence homology amino acid motifs protein sequence analysis eukaryotic cells