Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.

Computer Simulation of Liquids

2017 • 20,627 citations

Theory of simple liquids

1976 • 8,042 citations

Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent

1994 • 5,327 citations

Essential dynamics of proteins

1993 • 3,179 citations

Atomic charges derived from semiempirical methods

1990 • 3,157 citations

Solvent-Accessible Surfaces of Proteins and Nucleic Acids

1983 • 2,685 citations

AREAS, VOLUMES, PACKING, AND PROTEIN STRUCTURE

1977 • 2,631 citations

Analytical molecular surface calculation

1983 • 2,454 citations

An Introduction to Statistical Thermodynamics

1961 • 2,250 citations

Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models

1994 • 2,072 citations

Free energy calculations: Applications to chemical and biochemical phenomena

1993 • 2,045 citations

Electrostatic Interactions in Macromolecules: Theory and Applications

1990 • 1,324 citations

A scaled particle theory of aqueous and nonaqueous solutions

1976 • 1,255 citations

Residue – Residue Potentials with a Favorable Contact Pair Term and an Unfavorable High Packing Density Term, for Simulation and Threading

1996 • 1,243 citations

A new method for predicting binding affinity in computer-aided drug design

1994 • 1,154 citations

Calculation of conformational ensembles from potentials of mena force

1990 • 1,091 citations

Solvation thermodynamics of nonionic solutes

1984 • 958 citations

Hydrophobic bonding and accessible surface area in proteins

1974 • 887 citations

GEPOL: An improved description of molecular surfaces. III. A new algorithm for the computation of a solvent‐excluding surface

1994 • 835 citations

Method for estimating the configurational entropy of macromolecules

1981 • 831 citations

Large-amplitude nonlinear motions in proteins

1992 • 782 citations

Theory of hydrophobic bonding. II. Correlation of hydrocarbon solubility in water with solvent cavity surface area

1972 • 694 citations

Free Energy of Ionic Hydration

1996 • 661 citations

Computation of molecular volume

1985 • 590 citations

Macroscopic models of aqueous solutions: biological and chemical applications

1993 • 520 citations

Harmonic analysis of large systems. I. Methodology

1995 • 485 citations

Statistical Potentials Extracted From Protein Structures: How Accurate Are They?

1996 • 428 citations

Aspects of the Statistical Thermodynamics of Real Fluids

1960 • 409 citations

Atomic Radii for Continuum Electrostatics Calculations Based on Molecular Dynamics Free Energy Simulations

1997 • 393 citations

Statistical mechanics of chemical equilibria and intramolecular structures of nonrigid molecules in condensed phases

1976 • 329 citations

A Monte Carlo simulation of the hydrophobic interaction

1979 • 314 citations

The Contribution of Vibrational Entropy to Molecular Association

1994 • 312 citations

Structure-derived potentials and protein simulations

1996 • 288 citations

Empirical Correlation Between Hydrophobic Free Energy and Aqueous Cavity Surface Area

1974 • 284 citations

On the Validity of Electrostatic Linear Response in Polar Solvents

1996 • 279 citations

Computer Simulation of Hydrophobic Hydration Forces on Stacked Plates at Short Range

1995 • 272 citations

An Extended Linear Response Method for Determining Free Energies of Hydration

1995 • 262 citations

Numerical solution of the nonlinear Poisson–Boltzmann equation: Developing more robust and efficient methods

1995 • 247 citations

Experimental measurement of the effective dielectric in the hydrophobic core of a protein

1997 • 242 citations

Molecular basis for the Born model of ion solvation

1990 • 238 citations

Factors Influencing the Ability of Knowledge-based Potentials to Identify Native Sequence-Structure Matches

1994 • 211 citations

A boundary element method for molecular electrostatics with electrolyte effects

1990 • 208 citations

The rigorous computation of the molecular electric potential

1988 • 203 citations

Criteria that discriminate between native proteins and incorrectly folded models

1988 • 197 citations

SIRIUS

1990 • 193 citations

On the calculation of binding free energies using continuum methods: Application to MHC class I protein‐peptide interactions

1997 • 191 citations

Computing smooth molecular surfaces

1994 • 188 citations

Free energy of TIP4P water and the free energies of hydration of CH4 and Cl- from statistical perturbation theory

1989 • 186 citations

Solvation Free Energies Estimated from Macroscopic Continuum Theory: An Accuracy Assessment

1994 • 186 citations

A comparison of techniques for calculating protein essential dynamics

1997 • 174 citations

Improvements of the continuum model. 1. Application to the calculation of the vaporization thermodynamic quantities of nonassociated liquids

1988 • 169 citations

Gaussian fluctuation formula for electrostatic free-energy changes in solution

1991 • 168 citations

Hydration phenomena, classical electrostatics, and the boundary element method

1990 • 168 citations

Entropy in protein folding and in protein—protein interactions

1997 • 164 citations

Structure-derived hydrophobic potential

1992 • 163 citations

The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems

1995 • 158 citations

MSEED: A program for the rapid analytical determination of accessible surface areas and their derivatives

1992 • 157 citations

Free energy calculations of ion hydration: an analysis of the Born model in terms of microscopic simulations

1989 • 154 citations

A global model of the protein-solvent interface

1994 • 154 citations

Entropy Changes Accompanying Association Reactions of Proteins

1963 • 152 citations

A computer-simulation study of hydrophobic hydration of rare gases and of methane. I. Thermodynamic and structural properties

1991 • 151 citations

The size of molecules

1986 • 150 citations

Molecular Dynamics Study of the Dependence of Water Solvation Free Energy on Solute Curvature and Surface Area

1995 • 140 citations

A Fast Poisson Solver for Complex Geometries

1995 • 137 citations

Empirical potentials and functions for protein folding and binding

1997 • 137 citations

The Aqueous Solvation of Water: A Comparison of Continuum Methods with Molecular Dynamics

1994 • 132 citations

A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent

1997 • 131 citations

Solvent effects on protein association and protein folding

1990 • 129 citations

Comparison of database potentials and molecular mechanics force fields

1997 • 125 citations

SIMS: computation of a smooth invariant molecular surface

1997 • 121 citations

Occluded molecular surface: Analysis of protein packing

1995 • 117 citations

Thermodynamics of the Hydration Shell. 1. Excess Energy of a Hydrophobic Solute

1994 • 116 citations

Analysis of a large data base of electrostatic potential derived atomic charges

1992 • 108 citations

Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method qualitative estimates of free energy changes

1997 • 106 citations

Macromolecular electrostatic energy within the nonlinear Poisson–Boltzmann equation

1994 • 103 citations

Hydration free energy of water

1995 • 93 citations

Molecular surface area and hydrophobic effect

1992 • 93 citations

Treatment of electrostatic effects in proteins: Multigrid‐based newton iterative method for solution of the full nonlinear poisson–boltzmann equation

1994 • 89 citations

Adding backbone to protein folding: why proteins are polypeptides

1996 • 88 citations

Coupling Between Folding and Ionization Equilibria: Effects of pH on the Conformational Preferences of Polypeptides

1996 • 87 citations

Application of scaled particle theory to model the hydrophobic effect: implications for molecular association and protein stability

1994 • 87 citations

Harmonic analysis of large systems. III. Comparison with molecular dynamics

1995 • 85 citations

Finite-difference solution of the Poisson-Boltzmann equation: Complete elimination of self-energy

1996 • 84 citations

Finite difference Poisson-Boltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing

1997 • 84 citations

Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding

1995 • 81 citations

Discriminating compact nonnative structures from the native structure of globular proteins.

1995 • 76 citations

A combined iterative and boundary-element approach for solution of the nonlinear Poisson-Boltzmann equation

1992 • 74 citations

Harmonic analysis of large systems. II. Comparison of different protein models

1995 • 69 citations

SMART: A solvent-accessible triangulated surface generator for molecular graphics and boundary element applications

1995 • 66 citations

A fast and Space-efficient boundary element method for computing electrostatic and hydration effects in large molecules

1996 • 64 citations

An improved pair potential to recognize native protein folds

1994 • 49 citations

Determination of the conformation of folding initiation sites in proteins by computer simulation

1995 • 46 citations

Quantitative evaluation of hydration thermodynamics with a continuum model

1994 • 45 citations

Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy

1997 • 41 citations

Thermodynamics of a reverse turn motif. Solvent effects and side-chain packing

1997 • 39 citations

Multigrid methods in science and engineering

1996 • 28 citations

Energetic decomposition of the α-helix-coil equilibrium of a dynamic model system

1998 • 21 citations

Modeling hydrophobic solvation of nonspherical systems: Comparison of use of molecular surface area with accessible surface area

1997 • 20 citations

Electrostatic Field in Inhomogeneous Dielectric Media I. Indirect Boundary Element Method

1995 • 11 citations

Comparison of the Gibbs energy and entropy of interfaces water-n-hexane and water-perfluorotributylamine

1970 • 7 citations