Force Fields for Protein Simulations

作者: Jay W. Ponder , David A. Case

DOI: 10.1016/S0065-3233(03)66002-X

关键词:

摘要: Publisher Summary The chapter focuses on a general description of the force fields that are most commonly used at present, and it gives an indication directions current research may yield better functions in near future. After brief survey models, mostly generated during 1990s, focus is field taking developing new models. protein incorporate relatively simple potential energy function: emphasis use continuum methods to model electrostatic effects hydration introduction polarizability electronic response changes environment. Some history performance widely based equation simplest function or closely related equations reviewed. outlines some promising developments go beyond this, primarily by altering way interactions treated. atomic multipoles off-center charge distributions, as well attempts polarizability, also discussed chapter.

参考文章(248)
M. Born, Volumen und Hydratationswärme der Ionen European Physical Journal. ,vol. 1, pp. 45- 48 ,(1920) , 10.1007/BF01881023
Paul Beroza, David A. Case, Calculations of proton-binding thermodynamics in proteins. Methods in Enzymology. ,vol. 295, pp. 170- 189 ,(1998) , 10.1016/S0076-6879(98)95040-6
Michael Schaefer, Herman W.T. Van Vlijmen, Martin Karplus, Electrostatic contributions to molecular free energies in solution. Advances in Protein Chemistry. ,vol. 51, pp. 1- 57 ,(1998) , 10.1016/S0065-3233(08)60650-6
Frederick E. Petry, Principles and Applications Kluwer Academic Publishers. ,(1997)
Paul L. A. Popelier, Atoms in Molecules. An Introduction Harlow, Great Britain: Pearson Education; 2000.. ,(2000)
K. Rasmussen, S.R. Niketic, The Consistent Force Field: A Documentation ,(1977)
Benoit Roux, Masakatsu Watanabe, Alexander D. MacKerell, Oren M. Becker, Computational Biochemistry and Biophysics ,(2007)
Michael Levitt, Molecular dynamics of native protein. I. Computer simulation of trajectories. Journal of Molecular Biology. ,vol. 168, pp. 595- 617 ,(1983) , 10.1016/S0022-2836(83)80304-0