Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach

Authors:
K. C. Dukka Bahadur;Tatsuya Akutsu;Etsuji Tomita;Tomokazu Seki
Affiliations:
Kyoto University, Kyoto, Japan;Kyoto University, Kyoto, Japan;The University of Electro-Communications, Tokyo, Japan;The University of Electro-Communications, Tokyo, Japan
Venue:
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
Year:
2004

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Abstract

Protein side-chain packing has an important application in homology modeling, protein structure prediction, protein design, protein docking problems and many more.Protein side-chain packing problem is computationally known to be NP-hard (Akutsu, 1997) (Chazelle, Kingsford & Singh, 2003) (Pierce & Winfree, 2002). In the field of computer science, the notion of reduction of a problem to other problems is quite often used to design algorithms and to prove the complexity of a certain problem. In this work, we have used this notion of reduction to solve protein side-chain packing problem.We have developed a deterministic algorithm based approach to solve protein side-chain packing problem based on clique-based algorithms. For this, we reduced this problem to the maximum clique finding problem. Moreover, in order to incorporate the interaction preferences between the atoms, we have then extended this approach to maximum edge-weight clique finding problem by assigning weights based on probability discriminatory function. We have then solved this clique finding problem by using the clique finding algorithm developed by two of the authors (Tomita & Seki, 2003) and its variants (Suzuki, Tomita & Seki 2002).We have tested this approach to predict the side-chain conformations of a set of proteins and have compared the results with other existing methods. We have found considerable improvement in terms of the size of the proteins and in terms of the efficiency and accuracy of the prediction.