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Rapid protein structure classification using one-dimensional structure profiles on the bioSCAN parallel computer

Rapid protein structure classification using one-dimensional structure profiles on the bioSCAN parallel computer

Computer Applications in the Biosciences: Cabios 11(6): 675-679

ISSN/ISBN: 0266-7061

PMID: 8808584

DOI: 10.1093/bioinformatics/11.6.675

Rapid growth of protein structures database in recent years requires an effective approach for objective comparison and classification of deposited protein structures. We describe a novel method for structure comparison and classification based on the alignment of one-dimensional structure profiles. These profiles are obtained by calculating the O-C-C-O pseudodihedral angles (formed by O-C-C-O atoms of carbonyl groups of consecutive amino acidresidues) from protein three-dimensional coordinates. These angle measurements are then converted into a 24 letter alphabet, and the protein structures are represented by sequences of letter from this alphabet. The BioSCAN parallel computer, designed for primary sequence alignment, is used to rapidly align and classify these one-dimensional structure profiles. We have developed and implemented weighted scoring matrix to identify structural classes based on commonly found structural motifs. The results of our experiments are in good agreement with the traditional protein structure classification schemes. One-dimensional structure profiles significantly improve efficiency of structure comparison and classification.

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Accession: 009299116

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