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Updated: Jul 14, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Multiple methods for protein side chain packing using maximum weight cliques
J B Brown1, K C Dukka Bahadur, Etsuji Tomita
1Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, 611-0011 Kyoto, Japan. jbbrown@kuicr.kyoto-u.ac.jp
Abstract:
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.
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