Molecular dynamics simulations

Molecular dynamics with coupling to an external bath

1984 • 27,984 citations

Canonical dynamics: Equilibrium phase-space distributions

1985 • 20,411 citations

A molecular dynamics method for simulations in the canonical ensemble

1984 • 9,063 citations

Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling

1977 • 5,626 citations

Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K

2001 • 3,156 citations

Dynamics of folded proteins

1977 • 1,929 citations

A generalized reaction field method for molecular dynamics simulations

1995 • 1,386 citations

Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution

1998 • 1,336 citations

Climatic Impact of Tropical Lowland Deforestation on Nearby Montane Cloud Forests

2001 • 1,128 citations

An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase

2001 • 845 citations

Water Permeation Across Biological Membranes: Mechanism and Dynamics of Aquaporin-1 and GlpF

2001 • 844 citations

Energetics of ion conduction through the K+ channel

2001 • 768 citations

An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids

2000 • 751 citations

Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA

2001 • 688 citations

Local elevation: A method for improving the searching properties of molecular dynamics simulation

1994 • 548 citations

Ion permeation mechanism of the potassium channel

2000 • 423 citations

Non-Hamiltonian molecular dynamics: Generalizing Hamiltonian phase space principles to non-Hamiltonian systems

2001 • 351 citations

Molecular Dynamics of the KcsA K+ Channel in a Bilayer Membrane

2000 • 331 citations

Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model

2000 • 310 citations

Similarities between principal components of protein dynamics and random diffusion

2000 • 298 citations

Molecular Dynamics Simulation of the Kinetics of Spontaneous Micelle Formation

2000 • 293 citations

Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation

2000 • 279 citations

On the Truncation of Long-Range Electrostatic Interactions in DNA

2000 • 238 citations

Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches

1993 • 227 citations

Ueber eine veränderte Form des zweiten Hauptsatzes der mechanischen Wärmetheorie

1854 • 201 citations

Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling

2001 • 171 citations

Molecular Dynamics Simulations of Water with Novel Shell-Model Potentials

2001 • 169 citations

Mapping the early steps in the pH-induced conformational conversion of the prion protein

2001 • 167 citations

Molecular Dynamics Simulations of Pressure Effects on Hydrophobic Interactions

2001 • 150 citations

How to build a better pair potential for water

2001 • 144 citations

The potassium channel: Structure, selectivity and diffusion

2000 • 137 citations

Molecular Dynamics Simulation of the Structure of Dimyristoylphosphatidylcholine Bilayers with Cholesterol, Ergosterol, and Lanosterol

2001 • 132 citations

Accuracy of free-energy perturbation calculations in molecular simulation. II. Heuristics

2001 • 119 citations

Can Absolute Free Energies of Association Be Estimated from Molecular Mechanical Simulations? The Biotin−Streptavidin System Revisited

2001 • 111 citations

The effect of motional averaging on the calculation of NMR-derived structural properties

1999 • 103 citations

Simulations of the Estrogen Receptor Ligand-Binding Domain: Affinity of Natural Ligands and Xenoestrogens

2000 • 100 citations

Molecular Dynamics Study of Bacteriorhodopsin and the Purple Membrane

2001 • 93 citations

Molecular Dynamics Simulations of Human Prion Protein: Importance of Correct Treatment of Electrostatic Interactions

1999 • 93 citations

Molecular Dynamics Simulations of Wild-Type and Mutant Forms of the Mycobacterium tuberculosis MscL Channel

2001 • 92 citations

Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations.

2001 • 91 citations

Design, Synthesis, Computational Prediction, and Biological Evaluation of Ester Soft Drugs as Inhibitors of Dihydrofolate Reductase fromPneumocystis carinii

2001 • 90 citations

Calculation of Relative Binding Free Energy Differences for Fructose 1,6-Bisphosphatase Inhibitors Using the Thermodynamic Cycle Perturbation Approach

2001 • 79 citations

Studying the Dielectric Properties of a Protein Solution by Computer Simulation

2000 • 79 citations

Development of MD Engine: High-speed accelerator with parallel processor design for molecular dynamics simulations

1999 • 70 citations

Modeling ion–ion interaction in proteins: A molecular dynamics free energy calculation of the guanidinium-acetate association

2000 • 63 citations

Molecular Dynamics Generation of Nonarbitrary Membrane Models Reveals Lipid Orientational Correlations

2000 • 63 citations

Computational analysis of binding of P1 variants to trypsin

2001 • 56 citations

Comparison of different schemes to treat long‐range electrostatic interactions in molecular dynamics simulations of a protein crystal

2001 • 56 citations

Amplitudes and Frequencies of Protein Dynamics: Analysis of Discrepancies between Neutron Scattering and Molecular Dynamics Simulations

2000 • 55 citations

Reaction field, screening, and long-range interactions in simulations of ionic and dipolar systems

1994 • 52 citations

Free Energy, Entropy and Heat Capacity of the Hydrophobic Interaction as a Function of Pressure

2000 • 51 citations

Why Is It So Difficult To Simulate Entropies, Free Energies, and Their Differences?

2001 • 50 citations

Molecular dynamics simulations of antimicrobial peptides: From membrane binding to trans‐membrane channels

2001 • 45 citations

Structural Basis of Binding of High-Affinity Ligands to Protein Kinase C: Prediction of the Binding Modes through a New Molecular Dynamics Method and Evaluation by Site-Directed Mutagenesis

2001 • 44 citations

Conformational Averaging in pK Calculations: Improvement and Limitations in Prediction of Ionization Properties of Proteins

2001 • 43 citations

Molecular dynamics simulation and EPR spectroscopy of nitroxide side chains in bacteriorhodopsin

2000 • 42 citations

Functional Significance of Hierarchical Tiers in Carbonmonoxy Myoglobin: Conformational Substates and Transitions Studied by Conformational Flooding Simulations

2000 • 39 citations

Molecular Dynamics Study of HIV-1 Protease−Substrate Complex: Roles of the Water Molecules at the Loop Structures of the Active Site

2000 • 38 citations

Electrostatic Free Energy Calculations for Macromolecules: A Hybrid Molecular Dynamics/Continuum Electrostatics Approach

2000 • 38 citations

Simulation of Hydrated BPTI at High Pressure: Changes in Hydrogen Bonding and Its Relation with NMR Experiments

2000 • 32 citations

Free-Energy Calculations Highlight Differences in Accuracy between X-Ray and NMR Structures and Add Value to Protein Structure Prediction

2001 • 31 citations

Molecular dynamics simulation of adrenocorticotropin (1-10) peptide in a solvated dodecylphosphocholine micelle

2001 • 24 citations

Folding Studies of a Linear Pentamer Peptide Adopting a Reverse Turn Conformation in Aqueous Solution through Molecular Dynamics Simulation

2000 • 24 citations

Theoretical Studies Suggest a New Antifolate as a More Potent Inhibitor of Thymidylate Synthase

2000 • 19 citations

IBM promises scientists 500-fold leap in supercomputing power…

1999 • 17 citations

Sensitivity of an empirical affinity scoring function to changes in receptor–ligand complex conformations

2001 • 16 citations

Prediction of a ligand‐induced conformational change in the catalytic core of Cdc25A

1999 • 13 citations

Effect of the reaction field electrostatic term on the molecular dynamics simulation of the activation domain of procarboxypeptidase B

2000 • 11 citations

Molecular dynamics study of the dipalmitoyl phosphatidylcholine bilayer in the liquid crystal phase: an effect of the potential force fields on the membrane structure

2001 • 4 citations