By Harold A. Scheraga (auth.), Adam Liwo (eds.)
Since the second one 1/2 the twentieth century computing device computations have performed a serious function in technological know-how and engineering. Computer-based concepts became specifically vital in molecular biology, on account that they generally symbolize the one conceivable approach to achieve insights into the habit of a organic procedure as a complete. The complexity of organic structures, which generally has to be analyzed on varied time- and size-scales and with diverse degrees of accuracy, calls for the applying of alternative ways, starting from comparative research of sequences and structural databases, to the research of networks of interdependence among telephone parts and procedures, via coarse-grained modeling to atomically targeted simulations, and eventually to molecular quantum mechanics.
This booklet offers a complete evaluation of contemporary computer-based concepts for computing the constitution, houses and dynamics of biomolecules and biomolecular methods. The twenty-two chapters, written by way of scientists from around the world, handle the idea and perform of desktop simulation options within the examine of organic phenomena. The chapters are grouped into 4 thematic sections facing the next subject matters: the method of molecular simulations; purposes of molecular simulations; bioinformatics equipment and use of experimental info in molecular simulations; and chosen functions of molecular quantum mechanics. The booklet contains an introductory bankruptcy written through Harold A. Scheraga, one of many real pioneers in simulation experiences of biomacromolecules.
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Extra resources for Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics
Sample text
Comput. Methods to Study the Struct. & Dyn. of Biomolecules, SSBN 1, pp. 25–53. 1007/978-3-642-28554-7_2 © Springer-Verlag Berlin Heidelberg 2014 26 M. Blaszczyk et al. than studying the sequence. The best proofs for this statement are numbers. Currently (May 2012), the RefSeq database (Pruitt et al. 2007) contains almost 16 million sequences, while the total number of known structures in Protein Data Bank (Berman et al. 2003) is ca. 80 thousand. The main reason for such, and increasing disproportion is that experimental procedures for protein structure determination are very expensive and time-consuming and in many cases they simply cannot succeed.
Chem. : Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids. J. Phys. Chem. : Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H···O=C hydrogen bonds from packing configurations. J. Phys. Chem. : Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline containing peptides.
Chem. A. : Discretized model of proteins: I. Monte Carlo study of cooperativity in homopolypeptides. J. Chem. Phys. : Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field. J. Comput. Chem. : New optimization method for conformational energy calculations on polypeptides: Conformational space annealing. J. Comput. Chem. : Energy-based reconstruction of a protein backbone from its α-carbon trace by a Monte-Carlo method.