ArticleThe journal of physical chemistry. B2009
General library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic protein models.
Article in The journal of physical chemistry. B, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure.JACS Au · 2022Article
- From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field.Interface focus · 2019Review
- Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.Journal of chemical theory and computation · 2017Article
- Article
- Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins.Journal of chemical theory and computation · 2014Article
- OPTIMIZATION BIAS IN ENERGY-BASED STRUCTURE PREDICTION.Journal of theoretical & computational chemistry · 2013Article
- Article
- 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
- A versatile method for systematic conformational searches: application to CheY.Journal of computational chemistry · 2011Article
- Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space.Journal of computational chemistry · 2011Article
- Rapid sampling of all-atom peptides using a library-based polymer-growth approach.Journal of computational chemistry · 2011Article
- Equilibrium sampling in biomolecular simulations.Annual review of biophysics · 2011Review
- Thermal motions of the E. coli glucose-galactose binding protein studied using well-sampled, semi-atomistic simulations.Current topics in medicinal chemistry · 2011Article
- Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase.Journal of chemical theory and computation · 2010Article
- Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo.The journal of physical chemistry. B · 2010Article
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5 authors.
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Abstract
We introduce "library-based Monte Carlo" (LBMC) simulation, which performs Boltzmann sampling of molecular systems based on precalculated statistical libraries of molecular-fragment configurations, energies, and interactions. The library for each fragment can be Boltzmann distributed and thus account for all correlations internal to the fragment. LBMC can be applied to both atomistic and coarse-grained models, as we demonstrate in this "proof-of-principle" report. We first verify the approach in a toy model and in implicitly solvated all-atom polyalanine systems. We next study five proteins, up to 309 residues in size. On the basis of atomistic equilibrium libraries of peptide-plane configurations, the proteins are modeled with fully atomistic backbones and simplified Go-like interactions among residues. We show that full equilibrium sampling can be obtained in days to weeks on a single processor, suggesting that more accurate models are well within reach. For the future, LBMC provides a convenient platform for constructing adjustable or mixed-resolution models: the configurations of all atoms can be stored at no run-time cost, while an arbitrary subset of interactions is "turned on".
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