A Merge-Decoupling Dead End Elimination algorithm for protein side-chain conformation
by Ket Fah Chong, Hon Wai Leong
International Journal of Data Mining and Bioinformatics (IJDMB), Vol. 1, No. 4, 2007

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.

Online publication date: Mon, 02-Apr-2007

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