title: Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach.
abstract: "Protein Side-chain Packing" has an ever-increasing application in the field of bio-informatics, dating from the early methods of homology modeling to protein design and to the protein docking. However, this problem is computationally known to be NP-hard. In this regard, we have developed a novel approach to solve this problem using the notion of a maximum edge-weight clique. Our approach is based on efficient reduction of protein side-chain packing problem to a graph and then solving the reduced graph to find the maximum clique by applying an efficient clique finding algorithm developed by our co-authors. Since our approach is based on deterministic algorithms in contrast to the various existing algorithms based on heuristic approaches, our algorithm guarantees of finding an optimal solution. 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 that our results are favorably comparable or better than the results produced by the existing methods. As our test set contains a protein of 494 residues, we have obtained considerable improvement in terms of size of the proteins and in terms of the efficiency and the accuracy of prediction.
authors.affiliation: Graduate School of Informatics & Bioinformatics Center Kyoto University, Kyoto, 611-0001, Japan. dukka@kuicr.kyoto-u.ac.jp
authors.forename: K C
authors.initials: KC
authors.lastname: Dukka Bahadur
authors.forename: Etsuji
authors.initials: E
authors.lastname: Tomita
authors.forename: Jun'ichi
authors.initials: J
authors.lastname: Suzuki
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Akutsu
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D003461:Crystallography / Q000379:methods*; D016013:Likelihood Functions; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000032:analysis* / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins