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A CLP Approach to the Protein Side-Chain Placement Problem

  • Martin T. Swain
  • Graham J. L. Kemp
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2239)

Abstract

Selecting conformations for side-chains is an important subtask in building three-dimensional protein models. Side-chain placement is a difficult problem because of the large search space that has to be explored. We show that the side-chain placement problem can be expressed as a CLP program in which rotamer conformations are used as values for finite domain variables, and bad atomic clashes involving rotamers are represented as constraints. We present a new side-chain placement method that uses a series of automatically generated CLP programs to represent successively tighter side-chain packing constraints. By using these programs iteratively our method produces side-chain conformation predictions whose accuracy is comparable with that of other methods. The resulting system provides a testbed for evaluating the quality of protein models obtained using different domain enumeration heuristics and side-chain rotamer libraries.

Keywords

Minimum Probability Rotamer Library Root Mean Square Distance Rotamer Conformation Combinatorial Search Space 
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 2001

Authors and Affiliations

  • Martin T. Swain
    • 1
  • Graham J. L. Kemp
    • 1
  1. 1.Department of Computing ScienceUniversity of AberdeenAberdeenScotland

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