Multiple methods for protein side chain packing using maximum weight cliques.
In this paper, we present several methods for computing a solution to the protein side chain packing problem, with all methods having a common solution approach of breaking the polymer into subpolymers and using maximum edge weight cliques to prune the search space for the optimal side chain packing. We characterize the graph sizes generated for each method and compare their prediction accuracies. These methods are demonstrated for computing proteins up to approximately 8000 residues. In addition, we update a result published previously.
Brown
J B
JB
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, 611-0011 Kyoto, Japan. jbbrown@kuicr.kyoto-u.ac.jp
Dukka Bahadur
K C
KC
Tomita
Etsuji
E
Akutsu
Tatsuya
T
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry*; D011237:Predictive Value of Tests; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D009842:Oligopeptides; D011506:Proteins