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An Ant Colony Optimization Approach for the Protein Side Chain Packing Problem

by Hsin, Jing-Liang

Abstract (Summary)
The protein side chain prediction is an essential issue, in protein structure prediction, protein design, and protein docking problems. The protein side chain packing problem has been proved to be NP-hard. Our method for solving this problem is first to reduce it to the clique finding problem, and then we can apply the Ant Colony Optimization (ACO) algorithm to solve it. In knowledge-based methods, the rotamers are chosen from the rotamer library, which are based on the pair of dihedral angles, £r and £p, of backbones. We take the coordinate rotamer library as the template, so we do not need the complicated energy function to calculate the bond length and bond angle. We use a simple score function to evaluate the goodness of a solution of the ACO algorithm. The score function combines some factors, such as charge-charge interaction, intermolecular hydrogen bonds, disulfide bonds and van der Waals interactions. The experimental results show that our score function is biologically sensible. We compare our computational results with the results of SCWRL 3.0 and the residue-rotamer-reduction (R3) algorithm. The accuracy of our method outperforms both SCWRL 3.0 and R3 methods.
Bibliographical Information:

Advisor:Bang-ye Wu; Chung-Lung Cho; Chia-ning Yang; Yow-ling Shiue; Chang-biau Yang

School:National Sun Yat-Sen University

School Location:China - Taiwan

Source Type:Master's Thesis

Keywords:protein aco side chain structure prediction

ISBN:

Date of Publication:08/30/2006

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