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PEDS Advance Access originally published online on October 27, 2008
Protein Engineering Design and Selection 2008 21(12):729-735; doi:10.1093/protein/gzn056
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field

Meng Cui1,2,3, Mihaly Mezei1,3 and Roman Osman1

1Department of Structural and Chemical Biology, Mount Sinai School of Medicine, NYU, Box 1218, New York, NY 10029 2Department of Physiology and Biophysics, Virginia Commonwealth University, 1101 East Marshall Street, PO Box 980551, Richmond, VA 23298, USA

3 To whom correspondence should be addressed. E-mail: mcui{at}vcu.edu (M.C.); mihaly.mezei{at}mssm.edu (M.M.)

We have developed an improved local move Monte Carlo (LMMC) loop sampling approach for loop predictions. The method generates loop conformations based on simple moves of the torsion angles of side chains and local moves of backbone of loops. To reduce the computational costs for energy evaluations, we developed a grid-based force field to represent the protein environment and solvation effect. Simulated annealing has been used to enhance the efficiency of the LMMC loop sampling and identify low-energy loop conformations. The prediction quality is evaluated on a set of protein loops with known crystal structure that has been previously used by others to test different loop prediction methods. The results show that this approach can reproduce the experimental results with the root mean square deviation within 1.8 Å for all the test cases. The LMMC loop prediction approach developed here could be useful for improvement in the quality the loop regions in homology models, flexible protein–ligand and protein–protein docking studies.

Keywords: implicit solvent/local move Monte Carlo/potential map/protein loop prediction/simulated annealing

Received May 14, 2008; revised September 18, 2008; accepted September 23, 2008.


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