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2001
Springer

A CLP Approach to the Protein Side-Chain Placement Problem

9 years 6 months ago
A CLP Approach to the Protein Side-Chain Placement Problem
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.
Martin T. Swain, Graham J. L. Kemp
Added 28 Jul 2010
Updated 28 Jul 2010
Type Conference
Year 2001
Where CP
Authors Martin T. Swain, Graham J. L. Kemp
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