Open AccessDOMIRE: a web server for identifying structural domains and their neighbors in proteins
Author(s) -
Franck Samson,
Richard I. Shrager,
ChinHsien Tai,
Vichetra Sam,
Byung Kook Lee,
Peter J. Munson,
Jean-François Gibrat,
Jean Garnier
Publication year - 2012
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/bts076
Subject(s) - domain (mathematical analysis) , computer science , web server , protein domain , structural bioinformatics , protein structure database , protein structure , computational biology , structural alignment , data mining , sequence alignment , biology , world wide web , genetics , the internet , mathematics , sequence database , peptide sequence , gene , mathematical analysis , biochemistry
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.
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