Download Advance in Structural Bioinformatics by Dongqing Wei, Qin Xu, Tangzhen Zhao, Hao Dai PDF

By Dongqing Wei, Qin Xu, Tangzhen Zhao, Hao Dai

This textual content examines intimately mathematical and actual modeling, computational equipment and structures for acquiring and examining organic buildings, utilizing pioneering examine circumstances as examples. As such, it emphasizes programming and problem-solving talents. It presents details on constitution bioinformatics at a number of degrees, with person chapters overlaying introductory to complicated points, from basic tools and guidance on buying and studying genomics and proteomics sequences, the buildings of protein, DNA and RNA, to the fundamentals of actual simulations and strategies for conformation searches. This booklet could be of massive price to researchers and scholars within the fields of bioinformatics, computational biology and chemistry. Dr. Dongqing Wei is a Professor on the division of Bioinformatics and Biostatistics, collage of lifestyles technological know-how and Biotechnology, Shanghai Jiaotong college, Shanghai, China. His learn curiosity is within the basic zone of structural bioinformatics.

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J Chem Theory Comput 6:774–786 37. Gresh N, Cisneros GA, Darden TA, Piquemal JP (2007) Anisotropic, polarizable molecular mechanics studies of inter-and intramolecular interactions, and ligand-macromolecule complexes. A bottom-up strategy. J Chem Theory Comput 3:1960–1986 38. Ponder JW, Wu CJ, Ren PY, Pande VS, Chodera JD, Schnieders MJ et al (2010) Current status of the AMOEBA polarizable force field. J Phys Chem B 114:2549–2564 39. Engkvist O, Astrand PO, Karlstrom G (2000) Accurate intermolecular potentials obtained from molecular wave functions: bridging the gap between quantum chemistry and molecular simulations.

Allinger NL, Chen KH, Lii JH, Durkin KA (2003) Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compounds. J Comput Chem 24:1447–1472 8. Allured VS, Kelly CM, Landis CR (1991) SHAPES empirical force field: new treatment of angular potentials and its application to square-planar transition-metal complexes. J Am Chem Soc 113(1):1–12 9. Halgren TA (1996) Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules.

In the 1980s, molecular force fields such as AMBER, CHARMM, OPLS and GROMOS produce a positive impact on the research of life science, and promote the development of the molecular force fields targeting life science. Assisted model building with energy refinement (AMBER) force field. AMBER force field is one of the earliest molecular force field used for the research of biological macromolecules, and covers the simulations of proteins, DNA, monosaccharide and polysaccharide. In this force field, –CH2– and –CH3 are regard as united atom and used to treat hydrogen bonding interactions.

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