Biopolymer Structure Simulation and Optimization via Fragment Regrowth Monte Carlo

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Biopolymer Structure Simulation and Optimization via Fragment Regrowth Monte Carlo

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Title: Biopolymer Structure Simulation and Optimization via Fragment Regrowth Monte Carlo
Author: Kou, Samuel; Zhang, Jinfeng; Liu, Jun

Note: Order does not necessarily reflect citation order of authors.

Citation: Zhang, Jinfeng, Samuel C. Kou, and Jun S. Liu. 2007. Biopolymer structure simulation and optimization via fragment regrowth Monte Carlo. Journal of Chemical Physics 126(22): 225101.
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Abstract: An efficient exploration of the configuration space of a biopolymer is essential for its structure modeling and prediction. In this study, the authors propose a new Monte Carlo method, fragment regrowth via energy-guided sequential sampling (FRESS), which incorporates the idea of multigrid Monte Carlo into the framework of configurational-bias Monte Carlo and is suitable for chain polymer simulations. As a by-product, the authors also found a novel extension of the Metropolis Monte Carlo framework applicable to all Monte Carlo computations. They tested FRESS on hydrophobic-hydrophilic (HP) protein folding models in both two and three dimensions. For the benchmark sequences, FRESS not only found all the minimum energies obtained by previous studies with substantially less computation time but also found new lower energies for all the three-dimensional HP models with sequence length longer than 80 residues.
Published Version: http://dx.doi.org/10.1063/1.2736681
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:2766346

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  • FAS Scholarly Articles [7078]
    Peer reviewed scholarly articles from the Faculty of Arts and Sciences of Harvard University
 
 

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