Conformational sampling for the impatient

Replica-exchange molecular dynamics method for protein folding

1999 • 4,335 citations

Essential dynamics of proteins

1993 • 3,179 citations

T<scp>RANSITION</scp>P<scp>ATH</scp>S<scp>AMPLING</scp>: Throwing Ropes Over Rough Mountain Passes, in the Dark

2002 • 1,824 citations

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

1996 • 1,600 citations

Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model

2001 • 1,593 citations

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

1997 • 1,344 citations

A philosophical essay on probabilities

1952 • 1,145 citations

Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events

1997 • 940 citations

Parallel tempering algorithm for conformational studies of biological molecules

1997 • 913 citations

On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction

2002 • 785 citations

Large-amplitude nonlinear motions in proteins

1992 • 782 citations

Generalized-ensemble algorithms for molecular simulations of biopolymers

2001 • 759 citations

Absolute comparison of simulated and experimental protein-folding dynamics

2002 • 709 citations

Extending the Time Scale in Atomistic Simulation of Materials

2002 • 663 citations

Predicting slow structural transitions in macromolecular systems: Conformational flooding

1995 • 658 citations

Molecular dynamics simulations

2002 • 629 citations

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

1994 • 548 citations

Computational Biochemistry and Biophysics

2001 • 485 citations

Collective protein dynamics in relation to function

2000 • 411 citations

Principal Component Analysis and Long Time Protein Dynamics

1996 • 398 citations

The Role of Dynamics in Enzyme Activity

2003 • 345 citations

Exploring the energy landscape of a ? hairpin in explicit solvent

2001 • 342 citations

The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin

2001 • 338 citations

An Efficient Method for Sampling the Essential Subspace of Proteins

1996 • 301 citations

New Monte Carlo algorithms for protein folding

1999 • 286 citations

Structure of Met‐enkephalin in explicit aqueous solution using replica exchange molecular dynamics

2001 • 276 citations

Prediction of protein conformational freedom from distance constraints

1997 • 272 citations

Dynamics of large proteins through hierarchical levels of coarse‐grained structures

2001 • 228 citations

Collective Motions in HIV-1 Reverse Transcriptase: Examination of Flexibility and Enzyme Function

1999 • 206 citations

Algorithmic Challenges in Computational Molecular Biophysics

1999 • 193 citations

How to describe protein motion without amino acid sequence and atomic coordinates

2002 • 167 citations

Analysis of a 10-ns Molecular Dynamics Simulation of Mouse Acetylcholinesterase

2001 • 155 citations

Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds

2001 • 135 citations

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

1997 • 125 citations

Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems

2001 • 119 citations

Molecular Dynamics Simulations of Peptides and Proteins with Amplified Collective Motions

2003 • 112 citations

Self-Guided Molecular Dynamics Simulation for Efficient Conformational Search

1998 • 110 citations

Mathematical Analysis of Coupled Parallel Simulations

2001 • 109 citations

Long timescale simulations

2000 • 109 citations

Coordinates scaling and multiple time step algorithms for simulation of solvated proteins in the NPT ensemble

1998 • 108 citations

Hierarchy of structure loss in MD simulations of src SH3 domain unfolding

1999 • 95 citations

Simple bias potential for boosting molecular dynamics with the hyperdynamics scheme

1998 • 93 citations

Cooperative Fluctuations and Subunit Communication in Tryptophan Synthase

1999 • 91 citations

The energy landscape in non-biological and biological molecules

1998 • 88 citations

Molecular Dynamics Simulation of a Synthetic Ion Channel

1998 • 88 citations

Functional Motions of Influenza Virus Hemagglutinin: A Structure-Based Analytical Approach

2002 • 87 citations

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

2000 • 83 citations

Conformational changes in the chaperonin GroEL: new insights into the allosteric mechanism 1 1Edited by A. R. Fersht

1999 • 70 citations

Puddle-skimming: An efficient sampling of multidimensional configuration space

2002 • 61 citations

SWARM-MD: Searching Conformational Space by Cooperative Molecular Dynamics

1998 • 61 citations

Enhancing systematic motion in molecular dynamics simulation

1999 • 61 citations

Protein dynamics simulations from nanoseconds to microseconds

1999 • 61 citations

Self-guided enhanced sampling methods for thermodynamic averages

2003 • 58 citations

Energy landscape and fluctuations in proteins

2000 • 51 citations

Energy landscapes of conformationally constrained peptides

2001 • 48 citations

Computational Methods for Macromolecules: Challenges and Applications

2002 • 48 citations

Principal coordinate maps of molecular potential energy surfaces

1998 • 44 citations

Competitive and Reversible Binding of a Guest Molecule to Its Host in Aqueous Solution through Molecular Dynamics Simulation: Benzyl Alcohol/β-Cyclodextrin System

2002 • 40 citations

Time-Trimming Tricks for Dynamic Simulations

2001 • 40 citations

Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions

2003 • 39 citations

Multiple time step algorithms for molecular dynamics simulations of proteins: How good are they?

1998 • 39 citations

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

2000 • 39 citations

Conformational Flexibility of Pyruvate Dehydrogenase Complexes: A Computational Analysis by Quantized Elastic Deformational Model

2003 • 36 citations

Langevin dynamics of proteins at constant<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>p</mml:mi><mml:mi mathvariant="normal">H</mml:mi></mml:math>

2002 • 35 citations

Weighted-ensemble simulated annealing: Faster optimization on hierarchical energy surfaces

1997 • 35 citations

Conformational polymorphism of wild‐type and mutant prion proteins: Energy landscape analysis

2002 • 35 citations

Accelerated molecular dynamics of rare events using the local boost method

2001 • 35 citations

Efficient sampling in collective coordinate space

2000 • 34 citations

Computer Simulation Studies of Finite Temperature Conformational Equilibrium in Alanine-Based Peptides

1999 • 34 citations

Molecular dynamics of mouse and Syrian hamster PrP: Implications for activity

2000 • 33 citations

Puddle-jumping: a flexible sampling algorithm for rare event systems

2002 • 28 citations

Multiple time step diffusive Langevin dynamics for proteins

1998 • 23 citations

Modeling supramolecular assemblages

2002 • 22 citations

Multicopy molecular dynamics simulations suggest how to reconcile crystallographic and product formation data for camphor enantiomers bound to cytochrome P-450cam

2000 • 20 citations

Computational Molecular Biophysics Today: A Confluence of Methodological Advances and Complex Biomolecular Applications

1999 • 19 citations

Application of a Multiple Time Step Algorithm to Biomolecular Systems

1999 • 18 citations

Digitally filtered molecular dynamics: The frequency specific control of molecular dynamics simulations

2000 • 17 citations

Self-guided molecular dynamics in the isothermal–isobaric ensemble

2001 • 13 citations

Long time dynamics of Met-enkephalin: Tests of mode-coupling theory and implicit solvent models

2003 • 13 citations

Reversible Digitally Filtered Molecular Dynamics

2003 • 12 citations

Enlarging the landscape

2002 • 11 citations

Numerical calculations using the hyper-molecular dynamics simulation method

2001 • 10 citations

Exploring the idea of self-guided dynamics

2001 • 8 citations

Protein folding simulations and structure predictions

2001 • 8 citations

Exploring the natural conformational changes of the C-terminal domain of calmodulin

2002 • 7 citations