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Computational Modeling of Biological Systems: From Molecules by Yi Wang, J. Andrew McCammon (auth.), Nikolay V Dokholyan

24 February 2017 adminMathematics

By Yi Wang, J. Andrew McCammon (auth.), Nikolay V Dokholyan (eds.)

Computational modeling is rising as a robust new method of research and manage organic platforms. a number of tools were constructed to version, visualize, and rationally adjust platforms at a variety of size scales, ranging from molecular modeling and layout at atomic answer to mobile pathways modeling and research. larger time and size scale methods, equivalent to molecular evolution, have additionally vastly benefited from new breeds of computational methods. This ebook offers an outline of the validated computational tools used for modeling biologically and medically appropriate systems.

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Additional info for Computational Modeling of Biological Systems: From Molecules to Pathways

Example text

Model. 25, 247–260 (2006) 119. : Development and testing of a general AMBER force field. J. Comp. Chem. 25, 1157–1174 (2004) 120. : Exploring transmembrane diffusion pathways with molecular dynamics. Physiology 25, 142–154 (2010) 121. : Using selectively applied accelerated molecular dynamics to enhance free energy calculations. J. Chem. Theor. Comp. 6, 3285–3292 (2010) 122. : Coupling constant ph molecular dynamics with accelerated molecular dynamics. J. Chem. Theor. Comp. 6, 560–568 (2010) 123.

Opin. Struct. Biol. 19, 128–137 (2009) 67. : Docking and scoring in virtual screening for drug discovery: methods and applications. Nat. Rev. Drug Disc. 3, 939–945 (2004) 68. : Thermal Physics. W. H. Freeman, San Francisco (1980) 69. : Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J. Phys. Chem. B 114(23), 7830–7843 (2010) 70. : Virtual ligand screening: strategies, perspectives and limitations. Drug Discov. Today 11, 580–594 (2006) 28 Y. A. McCammon 71.

B 102, 3586–3616 (1998) 81. : Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comp. Chem. 25, 1400–1415 (2004) 82. : Electrostatics and diffusion of molecules in solution: simulations with the university of houston brownian dynamics program. Comput. Phys. Commun. 91, 57–95 (1995) 83. : Exploring multiple timescale motions in protein gb3 using accelerated molecular dynamics and nmr spectroscopy.

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