Protein-folding simulations in generalized ensembles
暂无分享,去创建一个
[1] N. Alves,et al. Partition function zeros and finite size scaling of helix-coil transitions in a polypeptide. , 2000, Physical review letters.
[2] Yuko Okamoto,et al. The Generalized-Ensemble Approach for Protein Folding Simulations , 1999 .
[3] Y. Okamoto,et al. GENERALIZED-ENSEMBLE MONTE CARLO METHOD FOR SYSTEMS WITH ROUGH ENERGY LANDSCAPE , 1997, cond-mat/9710306.
[4] Alan M. Ferrenberg,et al. New Monte Carlo technique for studying phase transitions. , 1988, Physical review letters.
[5] B. Berg,et al. Multicanonical algorithms for first order phase transitions , 1991 .
[6] K. Wüthrich,et al. The program FANTOM for energy refinement of polypeptides and proteins using a Newton – Raphson minimizer in torsion angle space , 1990 .
[7] C. Tsallis. Possible generalization of Boltzmann-Gibbs statistics , 1988 .
[8] Yuko Okamoto,et al. Effects of Side-Chain Charges on α-Helix Stability in C-Peptide of Ribonuclease A Studied by Multicanonical Algorithm , 1999 .
[9] U. Hansmann. Parallel tempering algorithm for conformational studies of biological molecules , 1997, physics/9710041.
[10] Ulrich H. E. Hansmann,et al. SMMP) A modern package for simulation of proteins , 2001 .
[11] Ulrich H E Hansmann,et al. Solvation model dependency of helix-coil transition in polyalanine. , 2002, Biophysical journal.
[12] W. Wenzel,et al. Stochastic Tunneling Approach for Global Minimization of Complex Potential Energy Landscapes , 1999 .
[13] H. Scheraga,et al. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[14] Yuko Okamoto,et al. Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple‐minima problem , 1993, J. Comput. Chem..
[15] U H Hansmann,et al. New Monte Carlo algorithms for protein folding. , 1999, Current opinion in structural biology.
[16] G. Torrie,et al. Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling , 1977 .
[17] H. Scheraga,et al. Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H...O = C hydrogen bonds from packing configurations , 1984 .
[18] P S Kim,et al. A thermostable 35-residue subdomain within villin headpiece. , 1996, Journal of molecular biology.
[19] Yuko Okamoto,et al. Tertiary Structure Prediction of C-Peptide of Ribonuclease A by Multicanonical Algorithm , 1998, physics/9806017.
[20] U. Hansmann. Protein folding simulations in a deformed energy landscape , 1999, physics/0001028.
[21] P. Kollman,et al. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. , 1998, Science.
[22] Ulrich H E Hansmann,et al. Global optimization by energy landscape paving. , 2002, Physical review letters.
[23] Y. Okamoto,et al. Finite-size scaling of helix–coil transitions in poly-alanine studied by multicanonical simulations , 1998 .
[24] K. Hukushima,et al. Exchange Monte Carlo Method and Application to Spin Glass Simulations , 1995, cond-mat/9512035.
[25] Shankar Kumar,et al. Method for free‐energy calculations using iterative techniques , 1996 .
[26] Ulrich H.E. Hansmann,et al. Helix formation and folding in an artificial peptide , 2002, cond-mat/0205559.
[27] B. Berg. Multicanonical recursions , 1995, hep-lat/9503019.
[28] D. Eisenberg,et al. Atomic solvation parameters applied to molecular dynamics of proteins in solution , 1992, Protein science : a publication of the Protein Society.
[29] Y. Okamoto,et al. Thermodynamics of Helix-Coil Transitions Studied by Multicanonical Algorithms , 1995, chem-ph/9505006.