By Oren M. Becker, Alexander D. MacKerell Jr., Benoit Roux, Masakatsu Watanabe
Masking theoretical equipment and computational innovations in biomolecular study, this ebook specializes in techniques for the remedy of macromolecules, together with proteins, nucleic acids, and bilayer membranes. It makes use of ideas in unfastened strength calculations, conformational research, response premiums, and transition pathways to calculate and interpret biomolecular houses gleaned from computer-generated membrane simulations. It additionally demonstrates comparative protein constitution modeling, outlines computer-aided drug layout, discusses Bayesian facts in molecular and structural biology, and examines the RISM-SCF/MCSCF method of chemical approaches in answer.
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Extra resources for Computational Biochemistry and Biophysics
Sample text
0. 09 based on the electrostatic contribution to the butane torsional surface [88], is justified by both the free energy of solvation of alkanes (S Fischer, M Karplus, personal communication) and the pure solvent properties of ethane being insensitive to the charge distribution. 115, based on the condensed phase properties of benzene [89], are used on all aromatic functional groups. , pyridine), where the carbon–hydrogen pairs adjacent to the heteroatom may have different charges; these charges would be determined via interactions with water as presented above.
99. DJ Tobias, K Tu, ML Klein. J Chim Phys 94:1482–1502, 1997. 100. TE Cheatham III, P Cieplak, PA Kollman. J Biomol Struct Dynam, 16:845–861, 1999. 101. LL Ho, AD MacKerell Jr, PA Bash. J Phys Chem 100:2588–2596, 1996. 102. PA Bash, LL Ho, AD MacKerell Jr, D Levine, P Hallstrom. Proc Natl Acad Sci USA 93: 3698–3703, 1996. 103. M Freindorf, J Gao. J Comput Chem 17:386–395, 1996. 104. LX Dang. J Phys Chem B 102:620–624, 1998. 105. SW Rick, BJ Berne. J Am Chem Soc 118:672–679, 1996. 106. P Linse, MA Carignano, G Karostro¨m.
1)]. Put in these terms, the classical equation of motion is written as a pair of coupled firstorder differential equations: r˙k ϭ ∂H(r, p) ; ∂pk ∂H(r, p) p˙k ϭ Ϫ ∂rk (8) By substituting the definition of H [Eq. (1)] into Eq. (8), we regain Eq. (6). The first first-order differential equation in Eq. , p i ϭ m i r˙ i ϭ m i v i , while the second turns into Eq. (6). A set of two first-order differential equations is often easier to solve than a single second-order differential equation. B. C). These properties are Conservation of energy.
Computational Biochemistry and Biophysics by Oren M. Becker, Alexander D. MacKerell Jr., Benoit Roux, Masakatsu Watanabe
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