An ant colony optimization approach for the protein side chain packing problem

Authors:
Jing-Liang Hsin;Chang-Biau Yang;Kuo-Si Huang;Chia-Ning Yang
Affiliations:
Department of Computer Science and Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan;Department of Computer Science and Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan;Department of Computer Science and Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan;Department of Medical Imaging and Radiological Sciences, I-Shou University, Kaohsiung, Taiwan
Venue:
MINO'07 Proceedings of the 6th conference on Microelectronics, nanoelectronics, optoelectronics
Year:
2007

Citing 2
Cited 1

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BEBI'09 Proceedings of the 2nd WSEAS international conference on Biomedical electronics and biomedical informatics

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Abstract

The protein side chain packing problem (PSCPP) is an essential issue for predicting structure in proteomics. PSCPP has been proved to be NP-hard. In this paper, we propose a method for solving PSCPP by transforming it to the graph clique problem, and then applying the ant colony optimization (ACO) algorithm to solve it. We build the coordinate rotamer library based on the pair of dihedral angles of backbones to reduce the required time. To evaluate the goodness of a solution of the ACO algorithm, we use a simple score function with four factors: disulfide bonds, intermolecular hydrogen bonds, charge-charge interactions 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 of them.