Databases

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

Found 168 links

Displaying 15 links

3D-FootprintDatabase Content

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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.

3didDatabase Content

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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.

AH-DBDatabase Content

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Database of protein structure pairs (apo-holo structure pairs) before and after binding. AH-DB is designed to provide an easy and unified way to prepare apo-holo structure pair data for studies. Data is generated by identifying/mapping molecules in Protein Data Bank (PDB) entries.

This content is being maintained by dirty.

ArachnoServer 2.0Database Content

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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.

ASDDatabase Content

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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.

ASPicDBDatabase Content

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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.

AtPIDDatabase Content

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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.

BioSystemsDatabase Content

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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.

links directory index: 34
TitlePublication YearGoogle Scholar Citation Count
The NCBI BioSystems database201034

BISCDatabase Content

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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.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
BISC: binary subcomplexes in proteins database20111

BRENDADatabase Content

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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.

links directory index: 60
TitlePublication YearGoogle Scholar Citation Count
BRENDA, the enzyme information system in 2011201160

BriXDatabase Content

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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.

BSDBDatabase Content

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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.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
BSDB: the biomolecule stretching database20114

BYKdbDatabase Content

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Bacterial protein tYrosine Kinase database (BYKdb). Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. However, BY-kinase sequence annotations in primary databases remain incomplete. This prompted us to develop a specialized database of computer-annotated BY-kinase sequences.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
BYKdb: the Bacterial protein tYrosine Kinase database20121

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