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

Scaling Concepts in Polymer Physics

1980 • 9,637 citations

Principles that Govern the Folding of Protein Chains

1973 • 6,771 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

Spin Glass Theory and Beyond

1988 • 2,992 citations

New Monte Carlo technique for studying phase transitions

1988 • 2,556 citations

Optimized Monte Carlo data analysis

1989 • 2,506 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

Protein Structure Prediction and Structural Genomics

2001 • 1,582 citations

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions

1997 • 1,403 citations

Effective energy function for proteins in solution

1999 • 1,269 citations

The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex

1997 • 1,250 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

Parallel tempering algorithm for conformational studies of biological molecules

1997 • 913 citations

Generalized-ensemble algorithms for molecular simulations of biopolymers

2001 • 759 citations

Multidimensional replica-exchange method for free-energy calculations

2000 • 693 citations

Calculation of protein conformations by proton-proton distance constraints

1985 • 564 citations

Dynamics of the Chaperonin ATPase Cycle: Implications for Facilitated Protein Folding

1994 • 461 citations

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

1999 • 433 citations

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

1996 • 353 citations

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

1999 • 341 citations

Ab Initio Protein Structure Prediction: Progress and Prospects

2001 • 325 citations

Water Dynamics: Fluctuation, Relaxation, and Chemical Reactions in Hydrogen Bond Network Rearrangement

1999 • 276 citations

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

2001 • 276 citations

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

2000 • 251 citations

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

2001 • 226 citations

Prospects for ab initio protein structural genomics

2001 • 196 citations

Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer

1999 • 193 citations

Three-helix-bundle protein in a Ramachandran model

2000 • 103 citations

Replica-exchange molecular dynamics simulation for supercooled liquids

2000 • 88 citations

Multi-Self-Overlap Ensemble for Protein Folding: Ground State Search and Thermodynamics

1999 • 84 citations

Solution structure of the albumin-binding GA module: a versatile bacterial protein domain

1997 • 83 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

Predicting protein three-dimensional structure

1999 • 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

Ab initio replica-exchange Monte Carlo method for cluster studies

2001 • 49 citations

Protein folding simulation with solvent-induced force field: Folding pathway ensemble of three-helix-bundle proteins

2000 • 46 citations

Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures

2001 • 16 citations

Physicochemical evaluation of protein folds predicted by threading

2001 • 13 citations