Generalized-ensemble algorithms for molecular simulations of biopolymers

Optimization by Simulated Annealing

1983 • 42,775 citations

Comparison of simple potential functions for simulating liquid water

1983 • 37,746 citations

Equation of State Calculations by Fast Computing Machines

1953 • 34,935 citations

MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures

1991 • 14,222 citations

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

1995 • 12,826 citations

The missing term in effective pair potentials

1987 • 12,201 citations

Possible generalization of Boltzmann-Gibbs statistics

1988 • 8,734 citations

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

1992 • 6,255 citations

Replica-exchange molecular dynamics method for protein folding

1999 • 4,335 citations

An all atom force field for simulations of proteins and nucleic acids

1986 • 3,388 citations

RASMOL: biomolecular graphics for all

1995 • 2,601 citations

New Monte Carlo technique for studying phase transitions

1988 • 2,556 citations

Raster3D Version 2.0. A program for photorealistic molecular graphics

1994 • 2,515 citations

Optimized Monte Carlo data analysis

1989 • 2,506 citations

Replica Monte Carlo Simulation of Spin-Glasses

1986 • 1,945 citations

Spin Glasses and Random Fields

1997 • 1,775 citations

Simulated Tempering: A New Monte Carlo Scheme

1992 • 1,767 citations

Exchange Monte Carlo Method and Application to Spin Glass Simulations

1996 • 1,749 citations

Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids

1975 • 1,532 citations

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

1992 • 1,528 citations

Monte Carlo-minimization approach to the multiple-minima problem in protein folding.

1987 • 1,419 citations

Optimized Cluster Expansions for Classical Fluids. II. Theory of Molecular Liquids

1972 • 1,329 citations

Multicanonical algorithms for first order phase transitions

1991 • 1,151 citations

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

1992 • 1,011 citations

Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids

1983 • 947 citations

Parallel tempering algorithm for conformational studies of biological molecules

1997 • 913 citations

The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies

1995 • 906 citations

Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides.

1987 • 737 citations

Multidimensional replica-exchange method for free-energy calculations

2000 • 693 citations

A fast algorithm for rendering space-filling molecule pictures

1988 • 616 citations

High-Strain-Rate Plastic Flow Studied via Nonequilibrium Molecular Dynamics

1982 • 611 citations

New Monte Carlo algorithm: Entropic sampling

1993 • 559 citations

An extended rism equation for molecular polar fluids

1981 • 552 citations

Generalized simulated annealing

1996 • 467 citations

Computing Science and Statistics

1999 • 395 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

Monte carlo study of the interacting self-avoiding walk model in three dimensions

1996 • 353 citations

Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H...O = C hydrogen bonds from packing configurations

1984 • 343 citations

Exploring the energy landscape of a ? hairpin in explicit solvent

2001 • 342 citations

Hyper-parallel tempering Monte Carlo: Application to the Lennard-Jones fluid and the restricted primitive model

1999 • 341 citations

New approach to spin-glass simulations

1992 • 316 citations

Energetic coupling between DNA bending and base pair opening.

1988 • 303 citations

Reducing quasi-ergodic behavior in Monte Carlo simulations by J-walking: Applications to atomic clusters

1990 • 301 citations

New Monte Carlo algorithms for protein folding

1999 • 286 citations

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

1996 • 286 citations

A site–site theory for finite concentration saline solutions

1992 • 276 citations

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

1987 • 273 citations

Dielectric effects in biopolymers: The theory of ionic saturation revisited

1985 • 253 citations

Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape

2000 • 251 citations

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

1998 • 243 citations

EXTENDED ENSEMBLE MONTE CARLO

2001 • 240 citations

Energy landscape of a native protein: Jumping-among-minima model

1998 • 237 citations

Replica-exchange Monte Carlo method for the isobaric–isothermal ensemble

2001 • 226 citations

Novel methods of sampling phase space in the simulation of biological systems

1997 • 219 citations

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

1994 • 219 citations

The isothermal/isobaric molecular dynamics ensemble

1983 • 207 citations

Thermodynamics of Helix-Coil Transitions Studied by Multicanonical Algorithms

1995 • 193 citations

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

1998 • 185 citations

Presto(protein engineering simulator): A vectorized molecular mechanics program for biopolymers

1992 • 180 citations

Numerical comparisons of three recently proposed algorithms in the protein folding problem

1997 • 168 citations

Generalized simulated annealing algorithms using Tsallis statistics: Application to conformational optimization of a tetrapeptide

1996 • 165 citations

New Monte Carlo Technique for Studying Phase Transitions

1989 • 154 citations

Phase changes in 38-atom Lennard-Jones clusters. II. A parallel tempering study of equilibrium and dynamic properties in the molecular dynamics and microcanonical ensembles

2000 • 150 citations

Monte Carlo Simulation and Global Optimization without Parameters

1995 • 134 citations

Comparative study of multicanonical and simulated annealing algorithms in the protein folding problem

1994 • 126 citations

Studies of an off-lattice model for protein folding: Sequence dependence and improved sampling at finite temperature

1995 • 122 citations

On Monte Carlo and molecular dynamics methods inspired by Tsallis statistics: Methodology, optimization, and application to atomic clusters

1997 • 116 citations

A direct comparison of helix propensity in proteins and peptides

1997 • 114 citations

Method for free‐energy calculations using iterative techniques

1996 • 113 citations

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

1997 • 112 citations

On the origin of the cooperativity of protein folding: Implications from model simulations

1996 • 110 citations

APPLICATION OF AN EXTENDED ENSEMBLE METHOD TO SPIN GLASSES

1996 • 107 citations

Conformational analysis of met‐enkephalin in both aqueous solution and in the presence of sodium dodecyl sulfate micelles using multidimensional NMR and molecular modeling

1992 • 104 citations

α-Helix folding by Monte Carlo simulated annealing in isolated C-peptide of ribonuclease A

1991 • 102 citations

THE GENERALIZED-ENSEMBLE APPROACH FOR PROTEIN FOLDING SIMULATIONS

1999 • 94 citations

Replica-exchange molecular dynamics simulation for supercooled liquids

2000 • 88 citations

Parallel excluded volume tempering for polymer melts

2000 • 88 citations

Molecular dynamics simulations of small peptides: Dependence on dielectric model and pH

1991 • 86 citations

Algorithmic aspects of multicanonical simulations

1998 • 85 citations

First-Principle Determination of Peptide Conformations in Solvents: Combination of Monte Carlo Simulated Annealing and RISM Theory

1998 • 82 citations

Effect of magnetic and nonmagnetic impurities (Ni, Zn) substitution for Cu in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Bi</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mo>(</mml:mo><mml:mi mathvariant="normal">SrCa</mml:mi><mml:mrow><mml:msub><mml:mrow><mml:mo>)</mml:mo></mml:mrow><mml:mrow><mml:mn>2</mml:mn><mml:mo>+</mml:mo><mml:mi>n</mml:mi></mml:mrow></mml:msub…

1997 • 81 citations

Domain-wall free energy of spin-glass models: Numerical method and boundary conditions

1999 • 81 citations

Replica-exchange simulated tempering method for simulations of frustrated systems

2000 • 80 citations

Multioverlap Simulations of the 3D Edwards-Anderson Ising Spin Glass

1998 • 79 citations

Monte Carlo simulations in generalized ensemble: Multicanonical algorithm versus simulated tempering

1996 • 78 citations

Simulation of Lattice Polymers with Multi-Self-Overlap Ensemble

1998 • 76 citations

Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures

2000 • 73 citations

Characteristic temperatures of folding of a small peptide

1997 • 71 citations

The folding funnel landscape for the peptide met-enkephalin

1999 • 69 citations

Two-component multicanonical Monte Carlo method for effective conformation sampling

1997 • 66 citations

Prediction of α-Helix Folding of Isolated C-Peptide of Ribonuclease A by Monte Carlo Simulated Annealing

1991 • 63 citations

Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95

2000 • 62 citations

Analytical rebridging Monte Carlo: Application to cis/trans isomerization in proline-containing, cyclic peptides

1999 • 60 citations

First-order phase transition in a stiff polymer chain

1997 • 59 citations

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

1995 • 59 citations

Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics simulation 1 1Edited by I. A. Wilson

1998 • 57 citations

Solvation structure and stability of peptides in aqueous solutions analyzed by the reference interaction site model theory

1997 • 55 citations

Monte Carlo study of the phase structure of compact polymer chains

1999 • 53 citations

Molecular mechanisms for cooperative folding of proteins

1998 • 50 citations

Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, β, and α/β proteins

1998 • 49 citations

Ab initio replica-exchange Monte Carlo method for cluster studies

2001 • 49 citations

Helix-coil transitions of amino-acid homo-oligomers in aqueous solution studied by multicanonical simulations

2000 • 48 citations

Multicanonical Monte Carlo study of solid-solid phase coexistence in a model colloid

1996 • 48 citations

Variation of the Energy Landscape of a Small Peptide under a Change from the ECEPP/2 Force Field to ECEPP/3

1997 • 46 citations

Peptide Conformations in Alcohol and Water: Analyses by the Reference Interaction Site Model Theory

2000 • 44 citations

New Monte Carlo Algorithm: Entropic Sampling

1993 • 43 citations

Carcinogen–base stacking and base–base stacking in dCpdG modified by (+) and (−) anti‐BPDE

1985 • 41 citations

Calculation of hydration free energy for a solute with many atomic sites using the RISM theory: A robust and efficient algorithm

1997 • 41 citations

Dependence on the dielectric model and pH in a synthetic helical peptide studied by Monte Carlo simulated annealing

1994 • 40 citations

The multicanonical weighted histogram analysis method for the free-energy landscape along structural transition paths

1999 • 40 citations

Effects of Side-Chain Charges on α-Helix Stability in C-Peptide of Ribonuclease A Studied by Multicanonical Algorithm

1999 • 39 citations

Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A

1998 • 39 citations

Calculation of solvation free energy using RISM theory for peptide in salt solution

1998 • 38 citations

Multicanonical procedure for continuum peptide models

2000 • 38 citations

Multicanonical Study of the 3D Ising Spin Glass

1993 • 37 citations

Improved protein free energy calculation by more accurate treatment of nonbonded energy: application to chymotrypsin inhibitor 2, V57A.

1998 • 36 citations

Multicanonical algorithm combined with the RISM theory for simulating peptides in aqueous solution

2000 • 36 citations

Multicanonical Monte Carlo Simulation of a Polymer with Stickers

1996 • 35 citations

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

1998 • 33 citations

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

1995 • 32 citations

Simulated annealing with Tsallis weights a numerical comparison

1997 • 30 citations

A Simple and Effective Procedure for Conformational Search of Macromolecules: Application to Met- and Leu-Enkephalin

1994 • 28 citations

Temperature dependence of distributions of conformations of a small peptide

1998 • 27 citations

Replica-ExchangeMonte Carlo Method for Ar Fluid

2000 • 21 citations

Structural Phase Transition of Di-Block Polyampholyte

1999 • 18 citations

Stochastic dynamics simulations in a new generalized ensemble

1998 • 17 citations

Tackling the protein folding problem by a generalized-ensemble approach with Tsallis statistics

1999 • 16 citations

Computational methods inspired by Tsallis statistics: Monte Carlo and molecular dynamics algorithms for the simulation of classical and quantum systems

1999 • 15 citations

Computing science and statistics : proceedings of the 23rd Symposium on the Interface, Seattle, Washington, April 21-24, 1991 ; Interface '91

1991 • 13 citations

α-Helix Propensities of Amino Acids Studied by Multicanonical Algorithm

1995 • 12 citations

A Multicanonical Monte Carlo Study of the 3D ±JSpin Glass

2000 • 12 citations

Adaptation and linear-response theory

1996 • 7 citations

Langevin Dynamics for Generalized Thermodynamics

2000 • 4 citations