Title: A Merge-Decoupling Dead End Elimination algorithm for protein side-chain conformation

Authors: Ket Fah Chong, Hon Wai Leong

Addresses: Department of Computer Science, National University of Singapore, 3 Science Drive 2, 117543, Singapore. ' Department of Computer Science, National University of Singapore, 3 Science Drive 2, 117543, Singapore

Abstract: Dead End Elimination (DEE) is a technique for eliminating rotamers that can not exist in any global minimum energy configuration for the protein side chain conformation problem. A popular method is Simple Goldstein DEE (SG-DEE) which is fast and eliminates rotamers by considering single residues for possible elimination. We present a Merge-Decoupling DEE (MD-DEE) that further reduces the number of rotamers after SG-DEE. MD-DEE works by forming residue-pairs but is fast and, like SG-DEE, is practical even for large proteins. Our experiments show that MD-DEE achieves further reduction in residue elimination (up to 25%) after SG-DEE.

Keywords: protein side-chain conformation; prediction; SCCP; dead end elimination; DEE; merge-decoupling algorithm; data mining; bioinformatics; rotamer elimination; residue elimination; global minimum energy; protein structure.

DOI: 10.1504/IJDMB.2007.012966

International Journal of Data Mining and Bioinformatics, 2007 Vol.1 No.4, pp.372 - 388

Published online: 02 Apr 2007 *

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