On-the-Fly Rotamer Pair Energy Evaluation in Protein Design

  • Andrew Leaver-Fay
  • Jack Snoeyink
  • Brian Kuhlman
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4983)


Most existing algorithms for protein design, including those in the Rosetta molecular modeling program, precompute energies for rotamer pairs, since these energies can be examined repeatedly. Simulated annealing algorithms, however, do not examine these energies with the same frequency; while some are examined many times, others may not be examined at all. This paper compares strategies for computing these energies on the fly and caching computed energy values that are likely to be reused. By avoiding the expense of computing pair energies that are not examined by simulated annealing, we show that some caching strategies not only improve running time in design, but also use 90% less memory, which allows design computations to be performed on memory-limited machines.


Simulated Annealing Protein Design Protein Structure Prediction Cache Strategy Pair Energy 
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 2008

Authors and Affiliations

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

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