ArticleThe journal of physical chemistry. B2010
Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo.
Article in The journal of physical chemistry. B, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units.Journal of chemical theory and computation · 2012Article
- Accelerating molecular Monte Carlo simulations using distance and orientation-dependent energy tables: tuning from atomistic accuracy to smoothed "coarse-grained" models.Journal of computational chemistry · 2012Article
- Expanding the conformational selection paradigm in protein-ligand docking.Methods in molecular biology (Clifton, N.J.) · 2012Article
- Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space.Journal of computational chemistry · 2011Article
- Equilibrium sampling in biomolecular simulations.Annual review of biophysics · 2011Review
- Automated sampling assessment for molecular simulations using the effective sample size.Journal of chemical theory and computation · 2010Article
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Authors and funding
3 authors.
Funding
Abstract
We applied our previously developed library-based Monte Carlo (LBMC) to equilibrium sampling of several implicitly solvated all-atom peptides. LBMC can perform equilibrium sampling of molecules using precalculated statistical libraries of molecular-fragment configurations and energies. For this study, we employed residue-based fragments distributed according to the Boltzmann factor of the optimized potential for liquid simulations all-atom (OPLS-AA) forcefield describing the individual fragments. Two solvent models were employed: a simple uniform dielectric and the generalized Born/surface area (GBSA) model. The efficiency of LBMC was compared to standard Langevin dynamics (LD) using three different statistical tools. The statistical analyses indicate that LBMC is more than 100 times faster than LD not only for the simple solvent model but also for GBSA.
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Registered trials
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