arrow

From NeuroLex

Jump to: navigation, search



Resource:Protein Data Bank Site

Name: Resource:Protein Data Bank Site
Description: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2014.

A database for structural and functional information on various protein sites (post-translational modification, catalytic active, organic and inorganic ligand binding, protein-protein, protein-DNA and protein-RNA interactions) in the Protein Data Bank (PDB). It was developed as a daughter database accumulating the data on functional and structural characteristics of functional sites stored in PDB, as well as their spatial surroundings.
It consists of functional sites extracted from PDB using the SITE records and of an additional set containing the protein interaction sites inferred from the contact residues in heterocomplexes. The PDBSite was set up by automated processing of the PDB. The PDBSite database can be queried through the functional description and the structural characteristics of the site and its environment. The PDBSite is integrated with the PDBSiteScan tool allowing structural comparisons of a protein against the functional sites. The PDBSite enables the recognition of functional sites in protein tertiary structures, providing annotation of function through structure.
The 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.
The data on biologically active protein sites are of extreme importance for solving many problems in molecular biology, biotechnology, and medicine. High specificity of biological activity in proteins is produced by unique structure of active sites that are often organized by a very complicate pattern. In particular, biologically active sites in proteins are often compiled out of remote by primary structure amino acid residues, which form compact clusters in the spatial structure with strictly ordered conformation. Specific structure and conformational parameters of these sites are determined by the structure of their spatial amino acid surroundings.
For example, spatial amino acid surroundings of enzyme catalytic centres determine the relief of hollows in catalytic centres of enzymes in a substrate binding regions, whereas the residues of antigen determinants of proteins determine their structure by organizing prominent parts at the protein surface. For many natural and mutant proteins, the relationships were found between protein activity and physico-chemical properties of amino acid residues composing the local surroundings of a functional site. The spatial surroundings of biologically active sites may be detected only if the data on tertiary protein structures are available. The Protein Data Bank (PDB) contains data on the spatial protein structures and their biologically active sites. 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.

Sponsor: This site is funded by GeneNetWorks.
Abbreviation: PDBSITE
Parent Organization: Siberian Branch of the Russian Academy of Sciences; Novosibirsk; Russia
Resource Type(s): Database
Resource: Resource
URL: http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsite/
*Id: nif-0000-21317
PMID: PMID 15608173
Uses: Resource:PDB
Availability: THIS RESOURCE IS NO LONGER IN SERVICE
Address: Institute of Cytology and Genetics SBRAS, Lavrentyev Avenue 10, Novosibirsk 630090, Russia
Keywords: 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
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Uncurated

This resource will be curated within 7 days.

For Resource Owners:
After the resource is curated, you may create a sitemap, which will help keep your registry description up-to-date and inform search engines about your resource.

Note: For a new resource, the website's URL must first be verified by a NIF curator before you may proceed.

Learn more about what NIF can do for your resource.
Proudly proclaim your inclusion in NIF by displaying the "Registered with NIF" button on your site. Please login to create the sitemap. (top right)

Notes

This page uses this default form:Resource



bookmark

*Note: Neurolex imports many terms and their ids from existing community ontologies, e.g., the Gene Ontology. Neurolex, however, is a dynamic site and any content beyond the identifier should not be presumed to reflect the content or views of the source ontology. Users should consult with the authoritative source for each ontology for current information.

Facts about Resource:Protein Data Bank SiteRDF feed
AbbrevPDBSITE  +
AddressInstitute of Cytology and Genetics SBRAS  +, Lavrentyev Avenue 10  +, Novosibirsk 630090  +, and Russia  +
AvailabilityTHIS RESOURCE IS NO LONGER IN SERVICE  +
CurationStatusuncurated  +
DefiningCitationhttp://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsite/  +
DefinitionTHIS RESOURCE IS NO LONGER IN SERVICE, doc THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2014.

A database for structural and functional information on various protein sites (post-translational modification, catalytic active, organic and inorganic ligand binding, protein-protein, protein-DNA and protein-RNA interactions) in the Protein Data Bank (PDB). It was developed as a daughter database accumulating the data on functional and structural characteristics of functional sites stored in PDB, as well as their spatial surroundings.
It consists of functional sites extracted from PDB using the SITE records and of an additional set containing the protein interaction sites inferred from the contact residues in heterocomplexes. The PDBSite was set up by automated processing of the PDB. The PDBSite database can be queried through the functional description and the structural characteristics of the site and its environment. The PDBSite is integrated with the PDBSiteScan tool allowing structural comparisons of a protein against the functional sites. The PDBSite enables the recognition of functional sites in protein tertiary structures, providing annotation of function through structure.
The 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.
The data on biologically active protein sites are of extreme importance for solving many problems in molecular biology, biotechnology, and medicine. High specificity of biological activity in proteins is produced by unique structure of active sites that are often organized by a very complicate pattern. In particular, biologically active sites in proteins are often compiled out of remote by primary structure amino acid residues, which form compact clusters in the spatial structure with strictly ordered conformation. Specific structure and conformational parameters of these sites are determined by the structure of their spatial amino acid surroundings.
For example, spatial amino acid surroundings of enzyme catalytic centres determine the relief of hollows in catalytic centres of enzymes in a substrate binding regions, whereas the residues of antigen determinants of proteins determine their structure by organizing prominent parts at the protein surface. For many natural and mutant proteins, the relationships were found between protein activity and physico-chemical properties of amino acid residues composing the local surroundings of a functional site. The spatial surroundings of biologically active sites may be detected only if the data on tertiary protein structures are available. The Protein Data Bank (PDB) contains data on the spatial protein structures and their biologically active sites. 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.

Sponsor: This site is funded by GeneNetWorks.
This site is funded by GeneNetWorks.
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +
Idnif-0000-21317  +
Is part ofSiberian Branch of the Russian Academy of Sciences; Novosibirsk; Russia  +
KeywordsEnzyme  +, 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  +, and Tertiary  +
LabelResource:Protein Data Bank Site  +
ModifiedDate18 August 2014  +
PMID15608173  +
Page has default formThis property is a special property in this wiki.Resource  +
SuperCategoryResource  +
UsesResource:PDB  +