Please use this identifier to cite or link to this item: http://scholarbank.nus.edu.sg/handle/10635/41577
Title: An of extension of dead end elimination for protein side-chain conformation using merge-decoupling
Authors: Ket, F.C.
Hon, W.L. 
Keywords: Algorithm
Protein side chain conformation
Issue Date: 2006
Source: Ket, F.C.,Hon, W.L. (2006). An of extension of dead end elimination for protein side-chain conformation using merge-decoupling. Proceedings of the ACM Symposium on Applied Computing 1 : 195-199. ScholarBank@NUS Repository.
Abstract: A two-phase strategy is widely adopted to solve the side-chain conformation prediction (SCCP) problem. Phase one is a fast reduction phase removing large numbers of rotamers not existing in the GMEC. Phase two (optimization phase) uses heuristics or exhaustive search to find a good/optimal solution. Presently, DEE (Dead End Elimination) is the only deterministic reduction method for phase one. However, to achieve convergence in phase two using DEE, the strategy of forming super-residues is used. This quickly leads to a combinatorial explosion, and becomes inefficient In this paper, an improvement of the DEE process by forming super-residues efficiently is proposed for phase one. The method basically merges residues into pairs based on some merging criteria. Simple Goldstein is then applied until no more elimination is possible. A decoupling process then reforms the original residues sans removed rotamers and rotamer pairs. The process of merging and elimination is repeated until no more elimination is possible. Initial experiments have shown the method, called Merge-Decoupling DEE, can fix up to 25% of the unfixed residues coming out of Simple Goldstein DEE. Copyright 2006 ACM.
Source Title: Proceedings of the ACM Symposium on Applied Computing
URI: http://scholarbank.nus.edu.sg/handle/10635/41577
ISBN: 1595931082
Appears in Collections:Staff Publications

Show full item record
Files in This Item:
There are no files associated with this item.

Page view(s)

37
checked on Jan 20, 2018

Google ScholarTM

Check


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.