By Oren M. Becker, Alexander D. MacKerell Jr., Benoit Roux, Masakatsu Watanabe

Protecting theoretical tools and computational thoughts in biomolecular examine, this booklet makes a speciality of methods for the remedy of macromolecules, together with proteins, nucleic acids, and bilayer membranes. It makes use of options in loose power calculations, conformational research, response charges, and transition pathways to calculate and interpret biomolecular homes gleaned from computer-generated membrane simulations. It additionally demonstrates comparative protein constitution modeling, outlines computer-aided drug layout, discusses Bayesian statistics in molecular and structural biology, and examines the RISM-SCF/MCSCF method of chemical techniques in resolution.

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H Guo, M Karplus. J Phys Chem 96:7273–7287, 1992. 60. FH Allen, S Bellard, MD Brice, BA Cartwright, A Doubleday, H Higgs, T Hummelink, BG Hummelink-Peters, O Kennard, WDS Motherwell, JR Rodgers, DG Watson. Acta Cryst B35: 2331–2339, 1979. 61. V Barone, M Cossi, J Tomasi. J Comput Chem 19:404–417, 1998. 62. EB Wilson Jr, JC Decius, PC Cross. Molecular Vibrations. New York: McGraw-Hill, 1955. 63. D Yin, AD MacKerell Jr. J Comput Chem 19:334–348, 1998. 64. AD MacKerell Jr. J Chim Phys 94:1436–1447, 1997.

15b) from Eq (15a) yields a complementary algorithm for propagating the velocities, vn ϭ r nϩ1 Ϫ r nϩ1 ϩ O(∆t 2) 2∆t (17) Figure 1a gives a graphical representation of the steps involved in a Verlet propagation. The algorithm embodied in Eqs. (16) and (17) provides a stable numerical method for solving Newton’s equation of motion for systems ranging from simple fluids to biopolymers. Like any algorithm, the Verlet algorithm has advantages as well as disadvantages.

2. CL Brooks III, M Karplus, BM Pettitt. Proteins, A Theoretical Perspective: Dynamics, Structure, and Thermodynamics, Vol 71. New York: Wiley, 1988. 3. JA McCammon, SC Harvey. Dynamics of Proteins and Nucleic Acids. New York: Cambridge Univ Press, 1987. 4. U Burkert, NL Allinger. Molecular Mechanics. Washington, DC: American Chemical Society, 1982. 5. A Blondel, M Karplus. J Comput Chem 17:1132–1141, 1996. 6. WE Reiher III. Theoretical Studies of Hydrogen Bonding. D. Thesis, Harvard University, 1985.

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