New Monte Carlo algorithms for protein folding

Optimization by Simulated Annealing

1983 • 42,775 citations

Adaptation in natural and artificial systems

1975 • 36,178 citations

Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images

1984 • 17,865 citations

Possible generalization of Boltzmann-Gibbs statistics

1988 • 8,734 citations

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

1977 • 5,626 citations

Hybrid Monte Carlo

1987 • 3,558 citations

New Monte Carlo technique for studying phase transitions

1988 • 2,556 citations

From Levinthal to pathways to funnels

1997 • 2,277 citations

THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective

1997 • 2,102 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

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

1987 • 1,419 citations

Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution

1998 • 1,336 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

Annealing Markov Chain Monte Carlo with Applications to Ancestral Inference

1995 • 840 citations

Protein Folding: A Perspective from Theory and Experiment

1998 • 840 citations

New Monte Carlo algorithm: Entropic sampling

1993 • 559 citations

Pruned-enriched Rosenbluth method: Simulations of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>θ</mml:mi></mml:math>polymers of chain length up to 1 000 000

1997 • 512 citations

Taboo Search: An Approach to the Multiple Minima Problem

1995 • 420 citations

Ring Closure and Local Conformational Deformations of Chain Molecules

1970 • 410 citations

Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties

1997 • 404 citations

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

1997 • 394 citations

Theoretical studies of protein-folding thermodynamics and kinetics

1997 • 387 citations

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

1993 • 385 citations

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

1990 • 301 citations

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

1996 • 286 citations

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

1998 • 185 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

A graph-theoretic algorithm for comparative modeling of protein structure

1998 • 157 citations

Efficient monte carlo method for simulation of fluctuating conformations of native proteins

1985 • 145 citations

Monte Carlo Simulation and Global Optimization without Parameters

1995 • 134 citations

Simulations of protein folding and unfolding

1998 • 134 citations

Application of the diffusion equation method for global optimization to oligopeptides

1992 • 129 citations

“Mining Minima”: Direct Computation of Conformational Free Energy

1997 • 128 citations

A comparison of heuristic search algorithms for molecular docking.

1997 • 124 citations

Genetic algorithms for protein structure prediction

1996 • 120 citations

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

1997 • 116 citations

Conformational Analysis of Flexible Molecules: Location of the Global Minimum Energy Conformation by the Simulated Annealing Method

1988 • 115 citations

Simulation methods for protein structure fluctuations

1980 • 113 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

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

1989 • 112 citations

Efficient Monte Carlo methods for the computer simulation of biological molecules

1992 • 110 citations

Assembly of protein structure from sparse experimental data: An efficient Monte Carlo model

1998 • 109 citations

Local interactions and protein folding: A three-dimensional off-lattice approach

1997 • 104 citations

Testing a new Monte Carlo algorithm for protein folding

1998 • 102 citations

THE GENERALIZED-ENSEMBLE APPROACH FOR PROTEIN FOLDING SIMULATIONS

1999 • 94 citations

Smart walking: A new method for Boltzmann sampling of protein conformations

1997 • 93 citations

Stochastic molecular optimization using generalized simulated annealing

1998 • 89 citations

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

1998 • 82 citations

Identifying the Tertiary Fold of Small Proteins with Different Topologies from Sequence and Secondary Structure using the Genetic Algorithm and Extended Criteria Specific for Strand Regions

1996 • 78 citations

Hybrid Monte Carlo simulations theory and initial comparison with molecular dynamics

1993 • 75 citations

Finite-size scaling of helix–coil transitions in poly-alanine studied by multicanonical simulations

1999 • 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

Reaching the global minimum in docking simulations: A Monte Carlo energy minimization approach using Bezier splines

1998 • 69 citations

Untitled

1997 • 66 citations

Local moves: An efficient algorithm for simulation of protein folding

1995 • 66 citations

Two-component multicanonical Monte Carlo method for effective conformation sampling

1997 • 66 citations

Formation of Helical States in Wormlike Polymer Chains

1998 • 64 citations

Highly Structured Searches with Quantum Computers

1998 • 59 citations

Identification of amino acid sequences with good folding properties in an off-lattice model

1997 • 58 citations

Molecular mechanisms for cooperative folding of proteins

1998 • 50 citations

Tertiary Structure Prediction of C-Peptide of Ribonuclease A by Multicanonical Algorithm

1998 • 41 citations

Conformational distribution of heptaalanine: Analysis using a new Monte Carlo chain growth method

1992 • 40 citations

Scaling behavior of stochastic minimization algorithms in a perfect funnel landscape

1999 • 40 citations

Efficient dynamics in the space of contact maps

1998 • 39 citations

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

1997 • 35 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

Monte Carlo Approach to Biopolymers and Protein Folding

1999 • 29 citations

Folding Pathways of a Helix−Turn−Helix Model Protein

1997 • 19 citations

A free energy based Monte Carlo minimization procedure for biomolecules

1994 • 16 citations

Free energy and stability of macromolecules studied by the double scanning simulation procedure

1990 • 14 citations

Conformational analysis of [Met5]-enkephalin: solvation and ionization considerations.

1998 • 13 citations

Finding the low-energy forms of avian pancreatic polypeptide with the diffusion-process-controlled Monte Carlo method

1998 • 13 citations

β-sheet formation in BPTI(16–36) by Monte Carlo simulated annealing

1999 • 13 citations

Efficiency of simulated annealing and the Monte Carlo minimization method for generating a set of low energy structures of peptides

1997 • 11 citations

Simulations of the thermodynamic properties of a short polyalanine peptide using potentials of mean force

1997 • 9 citations

Sampling potential energy surface of glycyl glycine peptide: Comparison of Metropolis Monte Carlo and stochastic dynamics

1998 • 3 citations