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• W2132005488 abstract "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." @default.
• W2132005488 created "2016-06-24" @default.
• W2132005488 creator A5009434832 @default.
• W2132005488 creator A5087424945 @default.
• W2132005488 creator A5091534914 @default.
• W2132005488 date "2008-10-27" @default.
• W2132005488 modified "2023-10-11" @default.
• W2132005488 title "Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field" @default.
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• W2132005488 doi "https://doi.org/10.1093/protein/gzn056" @default.
• W2132005488 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2597363" @default.
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• W2132005488 hasPublicationYear "2008" @default.
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