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Bioinformatics Advance Access published online on May 16, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl192
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received March 13, 2006
Revised May 4, 2006
Accepted May 14, 2006

Article

Developing a move-set for protein model refinement

Marc N. Offman 1, Paul W. Fitzjohn 1, and Paul A. Bates 1 *

1 Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories, London, WC2A 3PX, UK

* To whom correspondence should be addressed.
Paul A. Bates, E-mail: paul.bates{at}cancer.org.uk


  Abstract

Motivation: A wide variety of methods for the construction of an atomic model for a given amino acid sequence are known, the more accurate being those that use experimentally-determined structures as templates. However, far fewer methods are aimed at refining these models. The approach presented here carefully blends models created by several different means, in an attempt to combine the good quality regions from each into a final, more refined, model.

Results: We describe here a number of refinement operators (collectively, "move-set") that enable a relatively large region of conformational space to be searched. This is used within a genetic algorithm that reshuffles and repacks structural components. The utility of the move-set is demonstrated by introducing a cost function, containing both physical and other components guiding the input structures towards the target structure. We show that our move-set has the potential to improve the conformation of models and that this improvement can be beyond even the best template for some comparative modelling targets.

Availability: The POPULUS software package and source code is available at http://bmm.cancerresearchuk.org/~offman01/populus.html.

Associate Editor: Anna Tramontano
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