SCPC: a method to structurally compare protein complexes

• DOI: 10.1093/bioinformatics/btr654
• Publication Date: 2011-12-01T05:29:54Z
• Authors: Ryotaro Koike; Motonori Ota
• Keywords: Hemoglobins; 0303 health sciences; 03 medical and health sciences; Models, Chemical; Multiprotein Complexes; Databases, Protein; Protein Structure, Quaternary; Algorithms; Protein Structure, Secondary; Software

Abstract Motivation: Protein–protein interactions play vital functional roles in various biological phenomena. Physical contacts between proteins have been revealed using experimental approaches that solved the structures of protein complexes at atomic resolution. To examine huge number available Protein Data Bank, an efficient automated method compares is required. Results: We developed Structural Comparison Complexes (SCPC), a novel to structurally compare complexes. SCPC spatial arrangements subunits complex with those another secondary structure elements. Similar substructures are detected two and similarity scored. was applied dimers, homo-oligomers haemoglobins. properly estimated structural similarities dimers examined as well existing method, MM-align. Conserved were homo-tetramer homo-hexamer composed homologous proteins. Classification quaternary haemoglobins consistent conventional classification. The results demonstrate valuable tool investigate Availability: http://idp1.force.cs.is.nagoya-u.ac.jp/scpc/. Contact: [e-mail] Supplementary information: data Bioinformatics online.