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Bioinformatics Advance Access originally published online on March 6, 2007
Bioinformatics 2007 23(9):1099-1105; doi:10.1093/bioinformatics/btm073
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Andante: reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities

Richard E. Smith 1,*, Simon C. Lovell 1,{dagger}, David F. Burke 1, Rinaldo W. Montalvao 1 and Tom L. Blundell 1

1Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK

*To whom correspondence should be addressed.


  Abstract

Motivation: The accurate placement of side chains in computational protein modeling and design involves the searching of vast numbers of rotamer combinations.

Results: We have applied the information contained within structurally aligned homologous families, in the form of conserved {chi} angle conservation rules, to the problem of the comparative modeling. This allows the accurate borrowing of entire side-chain conformations and/or the restriction to high probability rotamer bins. The application of these rules consistently reduces the number of rotamer combinations that need to be searched to trivial values and also reduces the overall side-chain root mean square deviation (rmsd) of the final model. The approach is complementary to current side-chain placement algorithms that use the decomposition of interacting clusters to increase the speed of the placement process.

Contact: res50{at}mole.bio.cam.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger}Present address: University of Manchester, Faculty of Life Sciences, Michael Smith Building, Oxford Road, Manchester, M14 9PT.

Associate Editor: Anna Tramontano

Received on July 10, 2006; revised on February 21, 2007; accepted on February 25, 2007

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