Rotamer-pair energy calculations using a trie data structure

Authors:
Andrew Leaver-Fay;Brian Kuhlman;Jack Snoeyink
Affiliations:
Department of Computer Science, University of North Carolina at Chapel Hill;Department of Biochemistry, University of North Carolina at Chapel Hill;Department of Computer Science, University of North Carolina at Chapel Hill
Venue:
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Year:
2005

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Abstract

Protein design software places amino acid side chains by precomputing rotamer-pair energies and optimizing rotamer placement. If the software optimizes by rapid stochastic techniques, then the precomputation phase dominates run time. We present a new algorithm for rapid rotamer-pair energy computation that uses a trie data structure. The trie structure avoids redundant energy computations, and lends itself to time-saving pruning techniques based on a simple geometric criteria. With our new algorithm, we compute rotamer-pair energies nearly 4 times faster than the previous approach.