Protein folding pathways from replica exchange simulations and a kinetic network model.
暂无分享,去创建一个
[1] Ron Elber,et al. A method for determining reaction paths in large molecules: application to myoglobin , 1987 .
[2] Fumio Hirata,et al. Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water , 1990 .
[3] D. Gillespie. Markov Processes: An Introduction for Physical Scientists , 1991 .
[4] K. Dill,et al. Cooperativity in protein-folding kinetics. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[5] P. Argos,et al. Knowledge‐based protein secondary structure assignment , 1995, Proteins.
[6] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[7] J. Onuchic,et al. Theory of protein folding: the energy landscape perspective. , 1997, Annual review of physical chemistry.
[8] V. Muñoz,et al. Folding dynamics and mechanism of β-hairpin formation , 1997, Nature.
[9] Y. Amemiya,et al. Kinetic refolding of beta-lactoglobulin. Studies by synchrotron X-ray scattering, and circular dichroism, absorption and fluorescence spectroscopy. , 1998, Journal of molecular biology.
[10] 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.
[11] K. Dill. Polymer principles and protein folding , 1999, Protein science : a publication of the Protein Society.
[12] Y. Sugita,et al. Replica-exchange molecular dynamics method for protein folding , 1999 .
[13] A Kolinski,et al. Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques. , 1999, Biophysical journal.
[14] M. Karplus,et al. Understanding beta-hairpin formation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[15] Harold A. Scheraga,et al. Kinetics of cooperative protein folding involving two separate conformational families , 1999 .
[16] 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.
[17] S. Honda,et al. Role of side-chains in the cooperative beta-hairpin folding of the short C-terminal fragment derived from streptococcal protein G. , 2000, Biochemistry.
[18] Lorna J. Smith,et al. Understanding protein folding via free-energy surfaces from theory and experiment. , 2000, Trends in biochemical sciences.
[19] Lisa J. Lapidus,et al. Fast kinetics and mechanisms in protein folding. , 2000, Annual review of biophysics and biomolecular structure.
[20] D Thirumalai,et al. Mechanisms and kinetics of beta-hairpin formation. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[21] E I Shakhnovich,et al. Identifying the protein folding nucleus using molecular dynamics. , 1998, Journal of molecular biology.
[22] S. Honda,et al. Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus. , 2000, Journal of molecular biology.
[23] C. Batt,et al. Structural and kinetic characterization of early folding events in β-lactoglobulin , 2001, Nature Structural Biology.
[24] K. Sanbonmatsu,et al. Exploring the energy landscape of a β hairpin in explicit solvent , 2001 .
[25] 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.
[26] Eric J. Sorin,et al. β-hairpin folding simulations in atomistic detail using an implicit solvent model1 , 2001 .
[27] Charles L Brooks,et al. Protein and peptide folding explored with molecular simulations. , 2002, Accounts of chemical research.
[28] David Chandler,et al. Transition path sampling: throwing ropes over rough mountain passes, in the dark. , 2002, Annual review of physical chemistry.
[29] A. Fersht,et al. Protein Folding and Unfolding at Atomic Resolution , 2002, Cell.
[30] Ivet Bahar,et al. Fast‐folding protein kinetics, hidden intermediates, and the sequential stabilization model , 2002, Protein science : a publication of the Protein Society.
[31] M. Levitt,et al. Evidence of turn and salt bridge contributions to beta-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein G. , 2002, Biophysical chemistry.
[32] A. Fersht. On the simulation of protein folding by short time scale molecular dynamics and distributed computing , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[33] Emilio Gallicchio,et al. On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy. , 2003, Journal of the American Chemical Society.
[34] Michael R. Shirts,et al. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. , 2003, Biopolymers.
[35] S Banu Ozkan,et al. Computing the transition state populations in simple protein models. , 2003, Biopolymers.
[36] P. Bolhuis. Transition-path sampling of β-hairpin folding , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[37] R. Levy,et al. Free energy surfaces of β‐hairpin and α‐helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model , 2004 .
[38] J. Skolnick,et al. Reduced models of proteins and their applications , 2004 .
[39] Emilio Gallicchio,et al. The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute-solvent van der Waals interactions. , 2004, Biophysical chemistry.
[40] Y. Okamoto,et al. PROTEIN FORCE-FIELD PARAMETERS OPTIMIZED WITH THE PROTEIN DATA BANK II: COMPARISONS OF FORCE FIELDS BY FOLDING SIMULATIONS OF SHORT PEPTIDES , 2004 .
[41] Ronald M. Levy,et al. Long-time conformational transitions of alanine dipeptide in aqueous solution: Continuous and discrete-state kinetic models , 2004 .
[42] Ronald M. Levy,et al. AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high‐resolution modeling , 2004, J. Comput. Chem..
[43] David J Wales,et al. Folding of the GB1 hairpin peptide from discrete path sampling. , 2004, The Journal of chemical physics.
[44] Vijay S Pande,et al. Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. , 2004, The Journal of chemical physics.
[45] Guanghong Wei,et al. Complex folding pathways in a simple β‐hairpin , 2004 .
[46] William Swope,et al. Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a β-Hairpin Peptide† , 2004 .
[47] F. Rao,et al. The protein folding network. , 2004, Journal of molecular biology.
[48] William Swope,et al. Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory , 2004 .