Exploring the protein folding free energy landscape: coupling replica exchange method with P3ME/RESPA algorithm.

[1]  H. C. Andersen Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations , 1983 .

[2]  Wang,et al.  Nonuniversal critical dynamics in Monte Carlo simulations. , 1987, Physical review letters.

[3]  Alan M. Ferrenberg,et al.  Optimized Monte Carlo data analysis. , 1989, Physical Review Letters.

[4]  Akbar Nayeem,et al.  A comparative study of the simulated‐annealing and Monte Carlo‐with‐minimization approaches to the minimum‐energy structures of polypeptides: [Met]‐enkephalin , 1991 .

[5]  J. D. Doll,et al.  Extending J walking to quantum systems: Applications to atomic clusters , 1992 .

[6]  García,et al.  Large-amplitude nonlinear motions in proteins. , 1992, Physical review letters.

[7]  Mark E. Tuckerman,et al.  Reversible multiple time scale molecular dynamics , 1992 .

[8]  G. Parisi,et al.  Simulated tempering: a new Monte Carlo scheme , 1992, hep-lat/9205018.

[9]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[10]  L. Serrano,et al.  A short linear peptide that folds into a native stable β-hairpin in aqueous solution , 1994, Nature Structural Biology.

[11]  B. Berne,et al.  A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems , 1995 .

[12]  P. Argos,et al.  Knowledge‐based protein secondary structure assignment , 1995, Proteins.

[13]  K. Hukushima,et al.  Exchange Monte Carlo Method and Application to Spin Glass Simulations , 1995, cond-mat/9512035.

[14]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[15]  P. Procacci,et al.  Taming the Ewald sum in molecular dynamics simulations of solvated proteins via a multiple time step algorithm , 1996 .

[16]  B. Berne,et al.  Smart walking: A new method for Boltzmann sampling of protein conformations , 1997 .

[17]  P. Wolynes,et al.  Folding funnels and energy landscapes of larger proteins within the capillarity approximation. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Richard A. Friesner,et al.  Accurate ab Initio Quantum Chemical Determination of the Relative Energetics of Peptide Conformations and Assessment of Empirical Force Fields , 1997 .

[19]  B. Berne,et al.  Novel methods of sampling phase space in the simulation of biological systems. , 1997, Current opinion in structural biology.

[20]  K. Dill,et al.  From Levinthal to pathways to funnels , 1997, Nature Structural Biology.

[21]  V. Muñoz,et al.  Folding dynamics and mechanism of β-hairpin formation , 1997, Nature.

[22]  Christian Holm,et al.  How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines , 1998 .

[23]  M. Karplus,et al.  Protein Folding: A Perspective from Theory and Experiment. , 1998, Angewandte Chemie.

[24]  P. Kollman,et al.  Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. , 1998, Science.

[25]  V S Pande,et al.  Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Andrea Amadei,et al.  A molecular dynamics study of the 41‐56 β‐hairpin from B1 domain of protein G , 1999, Protein science : a publication of the Protein Society.

[27]  Dimensional Strategies and the Minimization Problem: Barrier-Avoiding Algorithms , 1999 .

[28]  A Kolinski,et al.  Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques. , 1999, Biophysical journal.

[29]  M. Karplus,et al.  Understanding beta-hairpin formation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[30]  R Nussinov,et al.  Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces. , 2000, Journal of molecular biology.

[31]  Yuji Sugita,et al.  Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape , 2000, cond-mat/0009119.

[32]  K. Sanbonmatsu,et al.  Exploring the energy landscape of a β hairpin in explicit solvent , 2001 .

[33]  B. Berne,et al.  The free energy landscape for β hairpin folding in explicit water , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Edward D Harder,et al.  Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems , 2001 .

[35]  Eric J. Sorin,et al.  β-hairpin folding simulations in atomistic detail using an implicit solvent model1 , 2001 .

[36]  A. Roitberg,et al.  All-atom structure prediction and folding simulations of a stable protein. , 2002, Journal of the American Chemical Society.

[37]  A. Roitberg,et al.  Smaller and faster: the 20-residue Trp-cage protein folds in 4 micros. , 2002, Journal of the American Chemical Society.

[38]  J. W. Neidigh,et al.  Designing a 20-residue protein , 2002, Nature Structural Biology.

[39]  K. Sanbonmatsu,et al.  α-Helical stabilization by side chain shielding of backbone hydrogen bonds , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[40]  B. Berne,et al.  Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water? , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[41]  V. Pande,et al.  The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations. , 2002, Journal of the American Chemical Society.

[42]  William Swope,et al.  Understanding folding and design: Replica-exchange simulations of ``Trp-cage'' miniproteins , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[43]  R. Zhou Free energy landscape of protein folding in water: Explicit vs. implicit solvent , 2003, Proteins.

[44]  R. Zhou Trp-cage: Folding free energy landscape in explicit water , 2003, Proceedings of the National Academy of Sciences of the United States of America.