Dataset Information

RefProtDom: a protein database with improved domain boundaries and homology relationships.

ABSTRACT:

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RefProtDom provides a set of divergent query domains, originally selected from Pfam, and full-length proteins containing their homologous domains, with diverse architectures, for evaluating pair-wise and iterative sequence similarity searches. Pfam homology and domain boundary annotations in the target library were supplemented using local and semi-global searches, PSI-BLAST searches, and SCOP and CATH classifications.

Availability

RefProtDom is available from http://faculty.virginia.edu/wrpearson/fasta/PUBS/gonzalez09a.

SUBMITTER: Gonzalez MW

PROVIDER: S-EPMC2935417 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature

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Publications

RefProtDom: a protein database with improved domain boundaries and homology relationships.

Gonzalez Mileidy W MW Pearson William R WR

Bioinformatics (Oxford, England) 20100806 18

<h4>Unlabelled</h4>RefProtDom provides a set of divergent query domains, originally selected from Pfam, and full-length proteins containing their homologous domains, with diverse architectures, for evaluating pair-wise and iterative sequence similarity searches. Pfam homology and domain boundary annotations in the target library were supplemented using local and semi-global searches, PSI-BLAST searches, and SCOP and CATH classifications.<h4>Availability</h4>RefProtDom is available from http://fa ...[more]

PMID: 20693322

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Project description:BackgroundMost proteins function by interacting with other molecules. Their interaction interfaces are highly conserved throughout evolution to avoid undesirable interactions that lead to fatal disorders in cells. Rational drug discovery includes computational methods to identify the interaction sites of lead compounds to the target molecules. Identifying and classifying protein interaction interfaces on a large scale can help researchers discover drug targets more efficiently.DescriptionWe introduce a large-scale protein domain interaction interface database called InterPare http://interpare.net. It contains both inter-chain (between chains) interfaces and intra-chain (within chain) interfaces. InterPare uses three methods to detect interfaces: 1) the geometric distance method for checking the distance between atoms that belong to different domains, 2) Accessible Surface Area (ASA), a method for detecting the buried region of a protein that is detached from a solvent when forming multimers or complexes, and 3) the Voronoi diagram, a computational geometry method that uses a mathematical definition of interface regions. InterPare includes visualization tools to display protein interior, surface, and interaction interfaces. It also provides statistics such as the amino acid propensities of queried protein according to its interior, surface, and interface region. The atom coordinates that belong to interface, surface, and interior regions can be downloaded from the website.ConclusionInterPare is an open and public database server for protein interaction interface information. It contains the large-scale interface data for proteins whose 3D-structures are known. As of November 2004, there were 10,583 (Geometric distance), 10,431 (ASA), and 11,010 (Voronoi diagram) entries in the Protein Data Bank (PDB) containing interfaces, according to the above three methods. In the case of the geometric distance method, there are 31,620 inter-chain domain-domain interaction interfaces and 12,758 intra-chain domain-domain interfaces.

Dataset Information

RefProtDom: a protein database with improved domain boundaries and homology relationships.

Unlabelled

Availability

Publications

RefProtDom: a protein database with improved domain boundaries and homology relationships.

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