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© Oxford University Press

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

D.L. Hoffman , S. Laiter 1, R.K. Singh 2, I.I. Vaisman 1 and A. Tropsha 1

Department of Computer Science, University of North Carolina at Chapel Hill CB #3175 Sitterson Hall, Chapel Hill, NC 27599-3175
1School of Pharmacy, University of North Carolina Chapel Hill, Laboratory for Molecular Modeling CB #7360 Beard Hall, Chapel Hill, NC 27599-7360 USA

2To whom correspondence should be addressed. Email. singh{at}cs.unc.edu

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 OCCO pseudodihedral angles (formed by O-C-C-O atoms of carbonyl groups of consecutive amino acid residues) 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 class 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.

Received on June 27, 1995; accepted on September 14, 1995

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