Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

1977 • 19,896 citations

<scp>CHARMM</scp>: A program for macromolecular energy, minimization, and dynamics calculations

1983 • 14,615 citations

The protein data bank: A computer-based archival file for macromolecular structures

1977 • 8,627 citations

The interpretation of protein structures: Estimation of static accessibility

1971 • 5,771 citations

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

1988 • 4,676 citations

A new force field for molecular mechanical simulation of nucleic acids and proteins

1984 • 4,553 citations

AREAS, VOLUMES, PACKING, AND PROTEIN STRUCTURE

1977 • 2,631 citations

Brownian dynamics with hydrodynamic interactions

1978 • 2,414 citations

An iterative solution method for linear systems of which the coefficient matrix is a symmetric 𝑀-matrix

1977 • 1,435 citations

Electrostatic Interactions in Macromolecules: Theory and Applications

1990 • 1,324 citations

A Leap-frog Algorithm for Stochastic Dynamics

1988 • 1,225 citations

Electromagnetic Theory

2015 • 1,123 citations

A simplified representation of protein conformations for rapid simulation of protein folding

1976 • 1,099 citations

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

1990 • 1,056 citations

Computer simulation of protein folding

1975 • 1,020 citations

Prediction of Ph-dependent Properties of Proteins

1994 • 811 citations

Theory of Protein Titration Curves. I. General Equations for Impenetrable Spheres

1957 • 798 citations

A consistent empirical potential for water–protein interactions

1984 • 763 citations

Electrostatics in biomolecular structure and dynamics

1990 • 695 citations

Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications

1981 • 614 citations

On the calculation of pK_as in proteins

1993 • 509 citations

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program

1991 • 442 citations

Faster superoxide dismutase mutants designed by enhancing electrostatic guidance

1992 • 387 citations

Brownian dynamics simulation of diffusion-influenced bimolecular reactions

1984 • 363 citations

The mechanism of action of superoxide dismutase from pulse radiolysis and electron paramagnetic resonance. Evidence that only half the active sites function in catalysis

1974 • 350 citations

Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation

1993 • 335 citations

Guidelines for the usage of incomplete decompositions in solving sets of linear equations as they occur in practical problems

1981 • 303 citations

Multiple‐site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins

1993 • 293 citations

The electric potential of a macromolecule in a solvent: A fundamental approach

1991 • 279 citations

Computer Simulations of the Diffusion of a Substrate to an Active Site of an Enzyme

1987 • 224 citations

On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase

1981 • 216 citations

Electrostatic interactions in the reaction mechanism of bovine erythrocyte superoxide dismutase.

1982 • 213 citations

A boundary element method for molecular electrostatics with electrolyte effects

1990 • 208 citations

Solving the finite difference linearized Poisson‐Boltzmann equation: A comparison of relaxation and conjugate gradient methods

1989 • 208 citations

Acetylcholinesterase: electrostatic steering increases the rate of ligand binding

1993 • 144 citations

Incorporating solvent and ion screening into molecular dynamics using the finite‐difference Poisson–Boltzmann method

1991 • 128 citations

Three-dimensional models of four mouse mast cell chymases. Identification of proteoglycan binding regions and protease-specific antigenic epitopes.

1993 • 128 citations

Point charge distributions and electrostatic steering in enzyme/substrate encounter: Brownian dynamics of modified copper/zinc superoxide dismutases

1990 • 123 citations

Electrophoretic and quasi-elastic light scattering of soluble protein-polyelectrolyte complexes

1993 • 120 citations

Dielectric boundary smoothing in finite difference solutions of the poisson equation: An approach to improve accuracy and convergence

1991 • 119 citations

Mutational studies of protein structures and their stabilities

1992 • 113 citations

Solving the finite‐difference non‐linear Poisson–Boltzmann equation

1992 • 107 citations

Segmental movement: definition of the structural requirements for loop closure in catalysis by triosephosphate isomerase

1992 • 98 citations

Helix–coil transitions in a simple polypeptide model

1980 • 97 citations

2.1 Å structure of Serratia endonuclease suggests a mechanism for binding to double-stranded DNA

1994 • 97 citations

Free energies of hydration of solute molecules. 4. Revised treatment of the hydration shell model

1988 • 96 citations

Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme

1993 • 91 citations

Slip boundary conditions and the hydrodynamic effect on diffusion controlled reactions

1976 • 89 citations

Simulation of the diffusion-controlled reaction between superoxide and superoxide dismutase. II. Detailed models.

1988 • 88 citations

Mutating the charged residues in the binding pocket of cellular retinoic acid‐binding protein simultaneously reduces its binding affinity to retinoic acid and increases its thermostability

1992 • 88 citations

Calculating electrostatic forces from grid‐calculated potentials

1990 • 86 citations

Effect of the Asn52 → Ile mutation on the redox potential of yeast cytochrome c

1992 • 82 citations

Electrostatic control of the rate-determining step of the copper, zinc, superoxide dismutase catalytic reaction

1987 • 75 citations

Load balancing on message passing architectures

1991 • 73 citations

Simulation of enzyme–substrate encounter with gated active sites

1994 • 73 citations

Poisson-Boltzmann analysis of the lambda repressor-operator interaction

1992 • 71 citations

Diffusional dynamics of ligand-receptor association

1986 • 69 citations

Electrostatic interactions stabilizing ferredoxin electron transfer complexes. Disruption by “conservative” mutations.

1992 • 68 citations

The incorporation of hydration forces determined by continuum electrostatics into molecular mechanics simulations

1991 • 68 citations

The nature of protein dipole moments: experimental and calculated permanent dipole of .alpha.-chymotrypsin

1989 • 65 citations

Dynamics of substrate binding to copper zinc superoxide dismutase

1985 • 62 citations

Molecular Dynamics Simulations in Heterogeneous Dielectrica and Debye-Hückel Media - Application to the Protein Bovine Pancreatic Trypsin Inhibitor

1992 • 54 citations

Electrostatic potentials and electrostatic interaction energies of rat cytochrome b5 and a simulated anion-exchange adsorbent surface

1994 • 52 citations

A Hydrodynamic Effect in the Rates of Diffusion-Controlled Reactions¹

1966 • 50 citations

The Role of Mobility in the Substrate Binding and Catalytic Machinery of Enzymes

1983 • 49 citations

Optimization of Brownian dynamics methods for diffusion-influenced rate constant calculations

1986 • 47 citations

Extended Brownian dynamics of diffusion controlled reactions

1985 • 45 citations

Molecular dynamics simulation of superoxide interacting with superoxide dismutase

1991 • 43 citations

Simulation of the bimolecular reaction between superoxide and superoxide dismutase: synthesis of the encounter and reaction steps

1993 • 38 citations

Brownian dynamics simulation of diffusion to irregular bodies

1987 • 38 citations

Brownian dynamics simulations of diffusional encounters between triose phosphate isomerase and glyceraldehyde phosphate: electrostatic steering of glyceraldehyde phosphate

1993 • 37 citations

Brownian dynamics simulations of molecular recognition in an antibody‐antigen system

1993 • 35 citations

The role of electrostatics in the binding of small ligands to enzymes

1987 • 35 citations

Inversion of receptor binding preferences by mutagenesis: Free energy thermodynamic integration studies on sugar binding to L-arabinose binding proteins

1993 • 31 citations

Regular representation of irregular charge distributions

1984 • 28 citations

Brownian dynamics simulation of diffusional encounters between triose phosphate isomerase and D-glyceraldehyde phosphate

1989 • 25 citations

A kinetic study of pig liver pyruvate kinase activated by fructose diphosphate

1974 • 24 citations

Brownian dynamics of diffusion-controlled reactions: the lattice method

1985 • 21 citations

Pfortran

1992 • 18 citations

Molecular Dynamics Simulation of Substrate-Enzyme Interactions in the Active Site Channel of Superoxide Dismutase

1993 • 17 citations

Trajectory simulation studies of diffusion-controlled reactions

1987 • 12 citations

Simulation of Bimolecular Reactions

1993 • 9 citations

Mobility and function in proteins and nucleic acids (Ciba Foundation Symposium 93)

1984 • 7 citations

Hydrodynamic boundary conditions and polymer dynamics

1976 • 6 citations

Correctness and determinism of parallel Monte Carlo processes

1992 • 5 citations

Parallel programming with guarded objects

1995 • 4 citations

Writing Good Software in Fortran

1988 • 4 citations

Zippier zaps: faster electrostatics calculations

1993 • 2 citations