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Rotamer-Pair Energy Calculations Using a Trie Data Structure

  • Andrew Leaver-Fay
  • Brian Kuhlman
  • Jack Snoeyink
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3692)

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.

Keywords

Heavy Atom Interaction Sphere Adaptive Dynamic Programming Rotamer Library Trie Node 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Andrew Leaver-Fay
    • 1
  • Brian Kuhlman
    • 2
  • Jack Snoeyink
    • 1
  1. 1.Department of Computer ScienceUniversity of North Carolina at Chapel Hill 
  2. 2.Department of BiochemistryUniversity of North Carolina at Chapel Hill 

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