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Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
The parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while theExpand
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.
TLDR
A complete set of intermolecular potential functions has been developed for use in computer simulations of proteins in their native environment and they have been parametrized directly to reproduce experimental thermodynamic and structural data on fluids. Expand
Potential energy functions for atomic-level simulations of water and organic and biomolecular systems.
An overview is provided on the development and status of potential energy functions that are used in atomic-level statistical mechanics and molecular dynamics simulations of water and of organic andExpand
OPLS all‐atom force field for carbohydrates
The OPLS all‐atom (AA) force field for organic and biomolecular systems has been expanded to include carbohydrates. Starting with reported nonbonded parameters of alcohols, ethers, and diols,Expand
Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding.
TLDR
It is concluded that the uncertainties from this source alone are sufficient to preclude the viability of current docking methodology for rank-ordering of diverse compounds in high-throughput virtual screening. Expand
Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field
The generalized Born/surface area (GB/SA) model of Still and co-workers was originally developed using partial atomic charges for organic molecules and ions from the OPLS united-atom force field. AnExpand
Performance of B3LYP Density Functional Methods for a Large Set of Organic Molecules.
TLDR
Gains in accuracy can be achieved by replacing energetics from NDO-based semiempirical methods with DFT results by evaluating the effect of an empirical dispersion correction term evaluated and found to improve agreement with the experimental data. Expand
Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field
TLDR
To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed, demonstrating significant improvement over previous OPLS-AA force fields. Expand
Prediction of the water content in protein binding sites.
TLDR
Testing of JAWS on five diverse examples demonstrates its accuracy in locating hydration sites in comparison to results from high-resolution crystal structures, and possible applications include aid in refinement of protein crystal structure, drug lead optimization, setup of docking calculations, and simulations of protein-ligand complexes. Expand
Optimization of azoles as anti-human immunodeficiency virus agents guided by free-energy calculations.
TLDR
FEP-guided lead optimization is confirmed as a valuable tool for molecular design including drug discovery; chlorine scans are particularly attractive since they are both straightforward to perform and highly informative. Expand
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