Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC

Marian Nanias; Maurizio Chinchio; Stanisław Ołdziej; Cezary Czaplewski; Harold A. Scheraga

doi:10.1002/jcc.20286

Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC

Journal of Computational Chemistry ◽

10.1002/jcc.20286 ◽

2005 ◽

Vol 26 (14) ◽

pp. 1472-1486 ◽

Cited By ~ 22

Author(s):

Marian Nanias ◽

Maurizio Chinchio ◽

Stanisław Ołdziej ◽

Cezary Czaplewski ◽

Harold A. Scheraga

Keyword(s):

Monte Carlo ◽

Protein Structure ◽

Force Field ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Replica Exchange ◽

Replica Exchange Monte Carlo

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Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems†

The Journal of Physical Chemistry B ◽

10.1021/jp030844f ◽

2004 ◽

Vol 108 (27) ◽

pp. 9421-9438 ◽

Cited By ~ 88

Author(s):

Adam Liwo ◽

Stanisław Ołdziej ◽

Cezary Czaplewski ◽

Urszula Kozłowska ◽

Harold A. Scheraga

Keyword(s):

Protein Structure ◽

Force Field ◽

Ab Initio ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Model Systems ◽

Energy Surfaces

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Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field

BMC Structural Biology ◽

10.1186/1472-6807-7-43 ◽

2007 ◽

Vol 7 (1) ◽

pp. 43 ◽

Cited By ~ 37

Author(s):

Sebastian Kmiecik ◽

Dominik Gront ◽

Andrzej Kolinski

Keyword(s):

Protein Structure ◽

High Resolution ◽

Force Field ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Reduced Models

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A Hierarchical Multiscale Approach to Protein Structure Prediction: Production of Low‐Resolution Packing Arrangements of Helices and Refinement of the Best Models with a United‐Residue Force Field

Multiscale Modeling and Simulation ◽

10.1137/060649318 ◽

2006 ◽

Vol 5 (4) ◽

pp. 1175-1195 ◽

Cited By ~ 4

Author(s):

M. Chinchio ◽

C. Czaplewski ◽

S. Ołdziej ◽

H. A. Scheraga

Keyword(s):

Protein Structure ◽

Force Field ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Multiscale Approach ◽

Low Resolution ◽

Hierarchical Multiscale

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De Novo Protein Structure Prediction by Combining Replica Exchange Simulations with Coevolutionary Data

Biophysical Journal ◽

10.1016/j.bpj.2017.11.3138 ◽

2018 ◽

Vol 114 (3) ◽

pp. 574a

Author(s):

Arthur Voronin ◽

Alexander Schug

Keyword(s):

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction ◽

De Novo ◽

Replica Exchange

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Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20133 ◽

2004 ◽

Vol 56 (3) ◽

pp. 475-486 ◽

Cited By ~ 40

Author(s):

Meng-Juei Hsieh ◽

Ray Luo

Keyword(s):

Protein Structure ◽

Force Field ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Scoring Function ◽

Implicit Solvent ◽

Amber Force Field ◽

Poisson Boltzmann

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

The Journal of Chemical Physics ◽

10.1063/1.1472510 ◽

2002 ◽

Vol 116 (20) ◽

pp. 9058-9067 ◽

Cited By ~ 515

Author(s):

Hiroaki Fukunishi ◽

Osamu Watanabe ◽

Shoji Takada

Keyword(s):

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Replica Exchange ◽

Biomolecular Systems ◽

Exchange Method ◽

Hamiltonian Replica Exchange ◽

Efficient Sampling ◽

Replica Exchange Method

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A Hybrid Monte Carlo Ant Colony Optimization Approach for Protein Structure Prediction in the HP Model

Electronic Proceedings in Theoretical Computer Science ◽

10.4204/eptcs.130.9 ◽

2013 ◽

Vol 130 ◽

pp. 61-69 ◽

Cited By ~ 2

Author(s):

Andrea G. Citrolo ◽

Giancarlo Mauri

Keyword(s):

Monte Carlo ◽

Protein Structure ◽

Ant Colony Optimization ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Ant Colony ◽

Optimization Approach ◽

Hybrid Monte Carlo ◽

Hp Model

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Protein Structure Prediction with a Combined Solvation Free Energy-Molecular Mechanics Force Field

Molecular Simulation ◽

10.1080/08927029308022162 ◽

1993 ◽

Vol 10 (2-6) ◽

pp. 121-149 ◽

Cited By ~ 57

Author(s):

Celia A. Schiffer ◽

James W. Caldwell ◽

Peter A. Kollman ◽

Robert M. Stroud

Keyword(s):

Free Energy ◽

Protein Structure ◽

Force Field ◽

Molecular Mechanics ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Solvation Free Energy

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1J1645 The reversible fragment assembly Monte Carlo method for ab initio-like protein structure prediction

Seibutsu Butsuri ◽

10.2142/biophys.42.s59_1 ◽

2002 ◽

Vol 42 (supplement2) ◽

pp. S59

Author(s):

G. Chikenji ◽

Y. Fujitsuka ◽

S. Takada

Keyword(s):

Monte Carlo ◽

Protein Structure ◽

Monte Carlo Method ◽

Ab Initio ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Fragment Assembly

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Fast Protein Structure Prediction Using Monte Carlo Simulations with Modal Moves

Journal of the American Chemical Society ◽

10.1021/ja036647b ◽

2003 ◽

Vol 125 (47) ◽

pp. 14244-14245 ◽

Cited By ~ 31

Author(s):

Paolo Carnevali ◽

Gergely Tóth ◽

Garrick Toubassi ◽

Siavash N. Meshkat

Keyword(s):

Monte Carlo ◽

Protein Structure ◽

Monte Carlo Simulations ◽

Protein Structure Prediction ◽

Structure Prediction

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