A targeted reweighting method for accelerating the exploration of high-dimensional configuration space.
暂无分享,去创建一个
[1] B. Berne,et al. Novel methods of sampling phase space in the simulation of biological systems. , 1997, Current opinion in structural biology.
[2] Wolfgang Wenzel,et al. Application of the stochastic tunneling method to high throughput database screening , 2003 .
[3] William H. Press,et al. Numerical Recipes: FORTRAN , 1988 .
[4] Helen M Berman,et al. Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif. , 2003, Journal of molecular biology.
[5] C. Branden,et al. Introduction to protein structure , 1991 .
[6] Jianpeng Ma,et al. A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. , 2004, Journal of molecular biology.
[7] S. Harrison,et al. DNA recognition by proteins with the helix-turn-helix motif. , 1990, Annual review of biochemistry.
[8] Y. Okamoto,et al. Numerical comparisons of three recently proposed algorithms in the protein folding problem , 1997 .
[9] H. Risken. The Fokker-Planck equation : methods of solution and applications , 1985 .
[10] Thomas Simonson,et al. Free energy simulations come of age: protein-ligand recognition. , 2002, Accounts of chemical research.
[11] Wilfred F. van Gunsteren,et al. When Are Free Energy Components Meaningful , 1994 .
[12] J. Banavar,et al. Computer Simulation of Liquids , 1988 .
[13] E. Helfand,et al. Numerical integration of stochastic differential equations — ii , 1979, The Bell System Technical Journal.
[14] Harold A. Scheraga,et al. Brownian dynamics simulations of protein folding , 1998 .
[15] J. Mccammon,et al. Dynamics of Proteins and Nucleic Acids , 2018 .
[16] Christian Bartels,et al. Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling , 1999 .
[17] J. Onuchic,et al. Understanding protein folding with energy landscape theory Part I: Basic concepts , 2002, Quarterly Reviews of Biophysics.
[18] Peter A. Kollman,et al. FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .
[19] R. Zwanzig. Nonequilibrium statistical mechanics , 2001, Physics Subject Headings (PhySH).
[20] W. Wenzel,et al. Stochastic Tunneling Approach for Global Minimization of Complex Potential Energy Landscapes , 1999 .
[21] J. Onuchic,et al. Funnels, pathways, and the energy landscape of protein folding: A synthesis , 1994, Proteins.
[22] R. Zwanzig,et al. Levinthal's paradox. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[23] M. Gilson,et al. The statistical-thermodynamic basis for computation of binding affinities: a critical review. , 1997, Biophysical journal.
[24] Régis Pomès,et al. Enhancing the accuracy, the efficiency and the scope of free energy simulations. , 2005, Current opinion in structural biology.
[25] Eric J. Sorin,et al. How well can simulation predict protein folding kinetics and thermodynamics? , 2005, Annual review of biophysics and biomolecular structure.
[26] H. Scheraga,et al. Macromolecular conformational dynamics in torsional angle space , 1998 .
[27] K. Dill,et al. From Levinthal to pathways to funnels , 1997, Nature Structural Biology.
[28] Ronald M. Levy,et al. Long-time conformational transitions of alanine dipeptide in aqueous solution: Continuous and discrete-state kinetic models , 2004 .
[29] Yuko Okamoto,et al. Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations. , 2003, Journal of molecular graphics & modelling.
[30] Peter Hänggi,et al. Gain in stochastic resonance: precise numerics versus linear response theory beyond the two-mode approximation. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.
[31] Bruce J. Berne,et al. Method for accelerating chain folding and mixing , 1993 .
[32] Jonathan W. Essex,et al. The development of replica-exchange-based free-energy methods , 2003 .
[33] G. Torrie,et al. Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid , 1974 .
[34] Haruki Nakamura,et al. Average energy guided simulated tempering implemented into molecular dynamics algorithm for protein folding simulation , 2004 .
[35] J. Onuchic,et al. DIFFUSIVE DYNAMICS OF THE REACTION COORDINATE FOR PROTEIN FOLDING FUNNELS , 1996, cond-mat/9601091.
[36] J. Durup,et al. On “Levinthal paradox” and the theory of protein folding , 1998 .
[37] P. Hänggi,et al. Reaction-rate theory: fifty years after Kramers , 1990 .
[38] J. Mongan,et al. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. , 2004, The Journal of chemical physics.
[39] Yuji Sugita,et al. Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape , 2000, cond-mat/0009119.
[40] U. Hansmann. Protein folding simulations in a deformed energy landscape , 1999, physics/0001028.
[41] Berend Smit,et al. Understanding molecular simulation: from algorithms to applications , 1996 .