The problem of compatible representatives
SIAM Journal on Discrete Mathematics
Side Chain-Positioning as an Integer Programming Problem
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
Fast and accurate algorithms for protein side-chain packing
Journal of the ACM (JACM)
A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies
INFORMS Journal on Computing
Minimum-weight triangulation is NP-hard
Journal of the ACM (JACM)
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We present in this study a new approach to code protein side-chain conformations into hexagon substructures. Classical side-chain packing methods consist of two steps: first, side-chain conformations, known as rotamers, are extracted from known protein structures as candidates for each residue; second, a searching method along with an energy function is used to resolve conflicts among residues and to optimize the combinations of side chain conformations for all residues. These methods benefit from the fact that the number of possible side-chain conformations is limited, and the rotamer candidates are readily extracted; however, these methods also suffer from the inaccuracy of energy functions. Inspired by threading and Ab Initio approaches to protein structure prediction, we propose to use hexagon substructures to implicitly capture subtle issues of energy functions. Our initial results indicate that even without guidance from an energy function, hexagon structures alone can capture side-chain conformations at an accuracy of 83.8 percent, higher than 82.6 percent by the state-of-art side-chain packing methods.