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Unformatted text preview: Journal of Bioinformatics and Computational Biology Vol. 2, No. 4 (2004) 699717 c Imperial College Press PAIRWISE PROTEIN STRUCTURE ALIGNMENT BASED ON AN ORIENTATION-INDEPENDENT BACKBONE REPRESENTATION JIEPING YE Department of Computer Science & Engineering University of Minnesota Minneapolis, MN 55455, USA email@example.com RAVI JANARDAN Department of Computer Science & Engineering University of Minnesota Minneapolis, MN 55455, USA firstname.lastname@example.org SONGTAO LIU Department of Mathematics University of Alberta Edmonton, Alberta T6G 2G1, Canada email@example.com Received 4 December 2003 1st Revision 16 March 2004 2nd Revision 16 April 2004 3rd Revision 19 April 2004 Accepted 20 April 2004 Determining structural similarities between proteins is an important problem since it can help identify functional and evolutionary relationships. In this paper, an algorithm is proposed to align two protein structures. Given the protein backbones, the algorithm finds a rigid motion of one backbone onto the other such that large substructures are matched. The algorithm uses a representation of the backbones that is independent of their relative orientations in space and applies dynamic programming to this represen- tation to compute an initial alignment, which is then refined iteratively. Experiments indicate that the algorithm is competitive with two well-known algorithms, namely DALI and LOCK. Keywords : Protein structure alignment; backbone representation; dynamic programming; optimization. 699 700 J. P. Ye, R. Janardan & S. T. Liu 1. Introduction Three-dimensional (3D) structure plays a central role in research directed towards understanding evolutionary and functional relationships among proteins. It is well- known that structural information is better conserved than sequence information in the evolution of proteins, 14 hence it can be used in the construction of phyloge- netic trees. 16 Protein-protein interactions are governed in large part by the shape, location, and composition of the so-called active sites. 2 The assignment of proteins to fold families is accomplished via structural analysis. 15 , 18 The need for effective structural analysis techniques has increased with the rapid growth in the number of 3D structures available now in the Protein Data Bank (PDB). 1 A key problem in protein structure analysis is pairwise protein structure align- ment: Given the C backbones of two proteins, the goal is to find a rigid motion of one backbone onto the other such that large, contiguous regions of the backbones are matched. (A formal definition is given later in Sec. 2.) Besides the applications mentioned above, pairwise structural alignment is also a key component of algo- rithms that seek to align multiple protein structures in order to find a core structure that captures essential structural information for the whole set....
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