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

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

ISBN-10: 7313110790

ISBN-13: 9787313110794

ISBN-10: 9401792445

ISBN-13: 9789401792448

ISBN-10: 9401792453

ISBN-13: 9789401792455

This textual content examines intimately mathematical and actual modeling, computational tools and structures for acquiring and examining organic constructions, utilizing pioneering study situations as examples. As such, it emphasizes programming and problem-solving abilities. It presents details on constitution bioinformatics at a variety of degrees, with person chapters protecting introductory to complicated features, from basic tools and instructions on buying and examining genomics and proteomics sequences, the constructions of protein, DNA and RNA, to the fundamentals of actual simulations and techniques for conformation searches. This publication might be of colossal worth 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, university of lifestyles technology and Biotechnology, Shanghai Jiaotong collage, Shanghai, China. His examine curiosity is within the common quarter of structural bioinformatics.

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Extra resources for Advance in Structural Bioinformatics

Example text

Develop the polarization force field of proteins and peptides [69], and they make use of SIBFA method to study the formamide nitrogen methylacetamide dimer and the hydrogen bonds energies of alanine, glycine residues. The results show that the addition of lone pair electrons or polar moment is better than the simple atoms central fix charge model in description and calculation the orientation and energy of hydrogen bond between the amide groups. In 2004, Patel et al. have developed the first generation of CHARMM fluctuating charge force field [70–74], which is mainly used to study the parameters of electrostatic model in proteins and peptides.

Proc Natl Acad Sci USA 105:6290–6295 63. Jiao D, Zhang J, Duke RE, Li G, Schnieders MJ, Ren P (2009) Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential. J Comput Chem 30:1701–1711 64. Shi Y, Jiao D, Schnieders MJ, Ren P (2009) Trypsin-ligand binding free energy calculation with AMOEBA. In: IEEE Engineering in Medicine and Biology Society, EMBC proceedings, pp 2328–2331 32 P. Xu et al. 65. Scherlis DA, Marzari N (2004) p-Stacking in charged thiophene oligomers.

Kaminski GA, Stern HA, Berne BJ, Friesner RA, Cao YX, Murphy RB et al (2002) Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests. J Comput Chem 23:1515–1531 62. Jiao D, Golubkov PA, Darden TA, Ren P (2008) Calculation of protein-ligand binding free energy by using a polarizable potential. Proc Natl Acad Sci USA 105:6290–6295 63. Jiao D, Zhang J, Duke RE, Li G, Schnieders MJ, Ren P (2009) Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential.

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

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