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DOMIRE: a web server for identifying structural domains and their neighbors in proteins.

ABSTRACT:

Summary

The DOMIRE web server implements a novel, automatic, protein structural domain assignment procedure based on 3D substructures of the query protein which are also found within structures of a non-redundant protein database. These common 3D substructures are transformed into a co-occurrence matrix that offers a global view of the protein domain organization. Three different algorithms are employed to define structural domain boundaries from this co-occurrence matrix. For each query, a list of structural neighbors and their alignments are provided. DOMIRE, by displaying the protein structural domain organization, can be a useful tool for defining protein common cores and for unravelling the evolutionary relationship between different proteins.

Availability

http://genome.jouy.inra.fr/domire

Contact

jean.garnier@jouy.inra.fr.

SUBMITTER: Samson F

PROVIDER: S-EPMC3315711 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature

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DOMIRE: a web server for identifying structural domains and their neighbors in proteins.

Samson Franck F Shrager Richard R Tai Chin-Hsien CH Sam Vichetra V Lee Byungkook B Munson Peter J PJ Gibrat Jean-François JF Garnier Jean J

Bioinformatics (Oxford, England) 20120215 7

<h4>Summary</h4>The DOMIRE web server implements a novel, automatic, protein structural domain assignment procedure based on 3D substructures of the query protein which are also found within structures of a non-redundant protein database. These common 3D substructures are transformed into a co-occurrence matrix that offers a global view of the protein domain organization. Three different algorithms are employed to define structural domain boundaries from this co-occurrence matrix. For each query ...[more]

PMID: 22345617

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