MBO(N)D: A multibody method for long-time molecular dynamics simulations

Molecular dynamics with coupling to an external bath

1984 • 27,984 citations

Computer Simulation of Liquids

2017 • 20,627 citations

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

1977 • 19,896 citations

Computer Simulation of Liquids

1988 • 15,963 citations

Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

1983 • 14,802 citations

A fast algorithm for particle simulations

1987 • 4,825 citations

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

1984 • 4,553 citations

Numerical Initial Value Problems in Ordinary Differential Equations

1973 • 4,016 citations

Semianalytical treatment of solvation for molecular mechanics and dynamics

1990 • 3,585 citations

Numerical Initial Value Problems in Ordinary Differential Equations

1972 • 3,569 citations

Reversible multiple time scale molecular dynamics

1992 • 3,392 citations

Essential dynamics of proteins

1993 • 3,179 citations

Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations

1983 • 2,842 citations

Adhesion Forces Between Individual Ligand-Receptor Pairs

1994 • 1,880 citations

Fluctuations and Irreversible Processes

1953 • 1,675 citations

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

1996 • 1,600 citations

Dynamics of Proteins and Nucleic Acids

1988 • 1,274 citations

Dynamics of Proteins and Nucleic Acids

1987 • 1,222 citations

Low-Barrier Hydrogen Bonds and Enzymic Catalysis

1994 • 1,117 citations

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

1991 • 929 citations

Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force

1996 • 913 citations

Kinematic and Dynamic Simulation of Multibody Systems

1994 • 789 citations

Molecular dynamics of liquid n-butane near its boiling point

1975 • 630 citations

Generalized Verlet Algorithm for Efficient Molecular Dynamics Simulations with Long-range Interactions

1991 • 603 citations

A Comprehensive Analytical Treatment of Continuum Electrostatics

1996 • 552 citations

Atomic solvation parameters applied to molecular dynamics of proteins in solution

1992 • 527 citations

Design, Activity, and 2.8 Å Crystal Structure of a C ₂ Symmetric Inhibitor Complexed to HIV-1 Protease

1990 • 524 citations

Advances in Chemical Physics

1988 • 496 citations

Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin

1998 • 455 citations

Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications

1989 • 439 citations

Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions

1992 • 419 citations

Solvation. A molecular dynamics study of a dipeptide in water

1979 • 406 citations

Principal Component Analysis and Long Time Protein Dynamics

1996 • 398 citations

Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement

1994 • 369 citations

Numerical Solution of Ordinary Differential Equations

1972 • 366 citations

Vibration Analysis of Structures by Component Mode Substitution

1971 • 339 citations

On Low-Barrier Hydrogen Bonds and Enzyme Catalysis

1995 • 313 citations

An Efficient Method for Sampling the Essential Subspace of Proteins

1996 • 301 citations

Effect of constraints on the dynamics of macromolecules

1982 • 293 citations

A Multiple-Time-Step Molecular Dynamics Algorithm for Macromolecules

1994 • 289 citations

Calculations of electrostatic energies in proteins

1985 • 270 citations

Reaction path study of conformational transitions in flexible systems: Applications to peptides

1990 • 252 citations

Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an α-helix

1984 • 240 citations

Protein hydration elucidated by molecular dynamics simulation.

1993 • 239 citations

Structure-based, C2 symmetric inhibitors of HIV protease

1990 • 213 citations

Multiple time-step methods in molecular dynamics

1978 • 209 citations

Calculation of classical trajectories with a very large time step: Formalism and numerical examples

1996 • 207 citations

Structure of the C-terminal domain of the ribosomal protein from Escherichia coli at 1.7 Å

1987 • 197 citations

The essential dynamics of thermolysin: Confirmation of the hinge‐bending motion and comparison of simulations in vacuum and water

1995 • 191 citations

A new approach for determining low‐frequency normal modes in macromolecules

1994 • 171 citations

A fast recursive algorithm for molecular dynamics simulation

1993 • 161 citations

Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations

1997 • 158 citations

Time dependence of atomic fluctuations in proteins: analysis of local and collective motions in bovine pancreatic trypsin inhibitor

1982 • 154 citations

Flap opening in HIV-1 protease simulated by ‘activated’ molecular dynamics

1995 • 150 citations

Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations

1995 • 149 citations

A molecular dynamics study of the C-terminal fragment of the ribosomal protein

1985 • 148 citations

Definitions and Nomenclature of Nucleic Acid Structure Parameters

1989 • 145 citations

Supercoiled DNA energetics and dynamics by computer simulation

1992 • 144 citations

Molecular Dynamics Simulation of DNA Stretching Is Consistent with the Tension Observed for Extension and Strand Separation and Predicts a Novel Ladder Structure

1996 • 142 citations

Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis

1994 • 129 citations

Self-avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems

1990 • 128 citations

Constant pressure-constant temperature molecular dynamics for rigid and partially rigid molecular systems

1985 • 127 citations

An Efficient Mean Solvation Force Model for Use in Molecular Dynamics Simulations of Proteins in Aqueous Solution

1996 • 126 citations

BIOMOLECULAR DYNAMICS AT LONG TIMESTEPS:Bridging the Timescale Gap Between Simulation and Experimentation

1997 • 125 citations

Projection of monte carlo and molecular dynamics trajectories onto the normal mode axes: Human lysozyme

1991 • 118 citations

New Methodology for Computer-Aided Modelling of Biomolecular Structure and Dynamics 1. Non-Cyclic Structures

1989 • 116 citations

Integration Methods for Molecular Dynamics

1996 • 99 citations

Molecular dynamics simulation with a continuum electrostatic model of the solvent

1995 • 97 citations

Dynamics of molecules with internal degrees of freedom by multiple time-step methods

1993 • 94 citations

Mathematical Approaches to Biomolecular Structure and Dynamics

1996 • 87 citations

Multiple Molecular Dynamics Simulations of the Anticodon Loop of tRNAAsp in Aqueous Solution with Counterions

1995 • 85 citations

Diagonalization in a mixed basis: A method to compute low‐frequency normal modes for large macromolecules

1993 • 73 citations

Anisotropy and anharmonicity of atomic fluctuations in proteins: Analysis of a molecular dynamics simulation

1987 • 73 citations

Simulations of Macromolecules by Multiple Time-Step Methods

1995 • 71 citations

Derivation and testing of explicit equations of motion for polymers described by internal coordinates

1991 • 71 citations

Peptide mechanics: A force field for peptides and proteins working with entire residues as smallest units

1992 • 70 citations

Molecular dynamics by the Backward‐Euler method

1989 • 68 citations

Towards an Exhaustive Sampling of the Configurational Spaces of the Two Forms of the Peptide Hormone Guanylin

1996 • 67 citations

LIN: A new algorithm to simulate the dynamics of biomolecules by combining implicit‐integration and normal mode techniques

1993 • 66 citations

Flexibility of the B-DNA backbone: effects of local and neighbouring sequences on pyrimidine-purine steps

1998 • 61 citations

Dynamics in Rugged Energy Landscapes with Applications to the S-Peptide and Ribonuclease A

1994 • 60 citations

Molecular mechanics parameters for organosilicon compounds calculated from ab initio computations

1988 • 60 citations

Methods of Component Mode Synthesis

1977 • 60 citations

Variable step molecular dynamics: An exploratory technique for peptides with fixed geometry

1990 • 57 citations

Homogenization of Hamiltonian systems with a strong constraining potential

1997 • 55 citations

Computer simulation of solid C60 using multiple time-step algorithms

1994 • 53 citations

Accurate DNA Dynamics without Accurate Long-Range Electrostatics

1998 • 45 citations

Dynamics of tyrosine ring rotations in a globular protein

1980 • 43 citations

Diffusion-influenced excimer formation kinetics

1991 • 43 citations

Long time scale molecular dynamics subspace integration method applied to anharmonic crystals and glasses

1993 • 42 citations

Novel methods for molecular dynamics simulations

1996 • 36 citations

Motions of an α‐helical polypeptide: Comparison of molecular and harmonic dynamics

1990 • 36 citations

Unfolding and refolding of the native structure of bovine pancreatic trypsin inhibitor studied by computer simulations

1993 • 35 citations

Collective motions in proteins investigated by X‐ray diffuse scattering

1994 • 35 citations

Protein molecular dynamics constrained to slow modes: theoretical approach based on a hierarchy of local modes with a set of holonomic constraints; the method and its tests on citrate synthase

1991 • 33 citations

On Multiple Time-step Algorithms and the Ewald Sum

1994 • 33 citations

Extracting the Energy Barrier Distribution of a Disordered System from the Instantaneous Normal Mode Density of States: Applications to Peptides and Proteins

1994 • 30 citations

Optical notch filter using thermotropic liquid crystalline polymers

1989 • 30 citations

Theoretical determination of conformational paths in citrate synthase

1992 • 27 citations

Virtual rigid body dynamics

1991 • 26 citations

Long timestep dynamics of peptides by the dynamics driver approach

1995 • 23 citations

Analyzing the normal mode dynamics of macromolecules by the component synthesis method

1992 • 22 citations

A molecular dynamics study of the C-terminal fragment of the L7/L12 ribosomal protein

1989 • 20 citations

Analyzing the normal mode dynamics of macromolecules by the component synthesis method: Residue clustering and multiple‐component approach

1994 • 14 citations

Model reduction methodology for articulated, multiflexible body structures

1994 • 8 citations

Ordinary differential equations of molecular dynamics

1994 • 7 citations

Low-Frequency Domain Motions in the Carboxy Terminal Fragment of L7/L12 Ribosomal Protein Studied with Molecular Dynamics Techniques: Are These Movements Model Independent?

1995 • 5 citations

Molecular dynamics simulations of siloxane-based side chain liquid crystalline polymers

1996 • 3 citations

Deleted Work

1955 • 0 citations