ArticleJournal of chemical theory and computation2014
COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Transmembrane Prostate Androgen-Induced Protein 1 Molecular Modeling and Refinement Using Coarse-Grained Molecular Dynamics.ACS omega · 2025Article
- Comparative Performance of Computer Simulation Models of Intrinsically Disordered Proteins at Different Levels of Coarse-Graining.Journal of chemical information and modeling · 2023Article
- Inverse Boltzmann Iterative Multi-Scale Molecular Dynamics Study between Carbon Nanotubes and Amino Acids.Molecules (Basel, Switzerland) · 2022Article
- Investigating Intrinsically Disordered Proteins With Brownian Dynamics.Frontiers in molecular biosciences · 2022Article
- Brownian Dynamics Simulations of Biological Molecules.Trends in chemistry · 2019Article
- Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.The journal of physical chemistry. B · 2017Article
- Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations.Journal of chemical theory and computation · 2017Article
- Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations.Journal of chemical theory and computation · 2017Article
- Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental-Computational Study.The journal of physical chemistry letters · 2017Article
- Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits.The Journal of chemical physics · 2015Article
- CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences.The Journal of chemical physics · 2015Article
- Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.Journal of chemical theory and computation · 2015Article
- Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field.Journal of chemical theory and computation · 2015Article
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2 authors.
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Abstract
We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions-which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)-quantitatively reproduced all of the "target" MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic (
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