Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling

Computer Simulation of Liquids

2017 • 20,627 citations

Canonical dynamics: Equilibrium phase-space distributions

1985 • 20,411 citations

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

1977 • 19,896 citations

Numerical recipes in C: the art of scientific computing

1993 • 18,639 citations

A unified formulation of the constant temperature molecular dynamics methods

1984 • 16,207 citations

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

1983 • 14,802 citations

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

1983 • 14,615 citations

MOLMOL: A program for display and analysis of macromolecular structures

1996 • 7,169 citations

THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method

1992 • 6,255 citations

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

1977 • 5,626 citations

New Monte Carlo technique for studying phase transitions

1988 • 2,556 citations

Optimized Monte Carlo data analysis

1989 • 2,506 citations

The calculation of the potential of mean force using computer simulations

1995 • 1,640 citations

Multicanonical ensemble: A new approach to simulate first-order phase transitions

1992 • 1,528 citations

Simulation of activation free energies in molecular systems

1996 • 1,279 citations

Transition path sampling and the calculation of rate constants

1998 • 1,031 citations

New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles

1992 • 1,011 citations

Packing Structures and Transitions in Liquids and Solids

1984 • 964 citations

Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics

1990 • 758 citations

New Monte Carlo algorithm: Entropic sampling

1993 • 559 citations

A Comprehensive Analytical Treatment of Continuum Electrostatics

1996 • 552 citations

Contribution of Hydration to Protein Folding Thermodynamics

1993 • 419 citations

Multicanonical Ensemble Generated by Molecular Dynamics Simulation for Enhanced Conformational Sampling of Peptides

1997 • 394 citations

Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple‐minima problem

1993 • 385 citations

Laser Temperature Jump Study of the Helix⇌Coil Kinetics of an Alanine Peptide Interpreted with a ‘Kinetic Zipper' Model

1997 • 349 citations

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations

1997 • 320 citations

Sampling ensembles of deterministic transition pathways

1998 • 297 citations

Molecular dynamics, Langevin and hydrid Monte Carlo simulations in a multicanonical ensemble

1996 • 286 citations

Adaptive umbrella sampling: Self-consistent determination of the non-Boltzmann bias

1987 • 273 citations

Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model

1998 • 243 citations

Monte Carlo Simulation of a First-Order Transition for Protein Folding

1994 • 219 citations

THE DIELECTRIC CONSTANT OF WATER AS A FUNCTION OF TEMPERATURE AND PRESSURE^1,2

1961 • 208 citations

Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy

1998 • 185 citations

Constant-temperature free energy surfaces for physical and chemical processes

1993 • 157 citations

Proton NMR studies of the solution conformations of an analog of the C-peptide of ribonuclease A

1989 • 154 citations

A comparative study of the simulated‐annealing and Monte Carlo‐with‐minimization approaches to the minimum‐energy structures of polypeptides: [Met]‐enkephalin

1991 • 149 citations

An adaptive umbrella sampling procedure in conformational analysis using molecular dynamics and its application to glycol

1992 • 147 citations

Estimating the relative populations of 310-helix and α-helix in Ala-rich peptides: a hydrogen exchange and high field NMR study

1997 • 120 citations

Prediction of the native conformation of a polypeptide by a statistical‐mechanical procedure. I. Backbone structure of enkephalin

1985 • 115 citations

Method for free‐energy calculations using iterative techniques

1996 • 113 citations

A prediction of tertiary structures of peptide by the Monte Carlo simulated annealing method

1989 • 112 citations

Generalized-ensemble Monte Carlo method for systems with rough energy landscape

1997 • 112 citations

Prediction of the native conformation of a polypeptide by a statistical‐mechanical procedure. II. average backbone structure of enkephalin

1986 • 111 citations

Molecular dynamics and Monte Carlo simulations favor the .alpha.-helical form for alanine-based peptides in water

1993 • 100 citations

310 Helixes in Peptides and Proteins As Studied by Modified Zimm-Bragg Theory

1995 • 82 citations

THE MULTICANONICAL ENSEMBLE: A NEW APPROACH TO COMPUTER SIMULATIONS

1992 • 73 citations

Two-component multicanonical Monte Carlo method for effective conformation sampling

1997 • 66 citations

Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide.

1995 • 59 citations

A selectively enhanced multicanonical molecular dynamics method for conformational sampling of peptides in realistic water molecules

1998 • 33 citations

Solution conformations of structured peptides: continuum electrostatics versus distance-dependent dielectric functions

1999 • 31 citations

Two dimensional umbrella sampling techniques for the computer simulation study of helical peptides at thermal equilibrium: The 3K(I) peptide in vacuo and solution

1998 • 29 citations

Characterization of flexible molecules in solution: the RGDW peptide 1 1Edited by B. Honig

1998 • 26 citations

Adaptive umbrella sampling of the potential energy: modified updating procedure of the umbrella potential and application to peptide folding

1999 • 16 citations

Multi-dimensional entropy sampling Monte Carlo method and free energy landscape of Ar13

1997 • 5 citations