Download Computational Methods to Study the Structure and Dynamics of by Harold A. Scheraga (auth.), Adam Liwo (eds.) PDF

By Harold A. Scheraga (auth.), Adam Liwo (eds.)

Since the second one 1/2 the 20 th century computer computations have performed a severe function in technological know-how and engineering. Computer-based ideas became specially vital in molecular biology, on the grounds that they generally signify the one workable option to achieve insights into the habit of a organic procedure as a complete. The complexity of organic structures, which generally should be analyzed on diverse time- and size-scales and with assorted degrees of accuracy, calls for the appliance of other techniques, starting from comparative research of sequences and structural databases, to the research of networks of interdependence among phone parts and methods, via coarse-grained modeling to atomically designated simulations, and at last to molecular quantum mechanics.

This e-book presents a complete review of recent computer-based thoughts for computing the constitution, homes and dynamics of biomolecules and biomolecular strategies. The twenty-two chapters, written by means of scientists from worldwide, handle the speculation and perform of computing device simulation strategies within the learn of organic phenomena. The chapters are grouped into 4 thematic sections facing the next themes: the method of molecular simulations; functions of molecular simulations; bioinformatics equipment and use of experimental info in molecular simulations; and chosen purposes of molecular quantum mechanics. The booklet contains an introductory bankruptcy written by means of Harold A. Scheraga, one of many real pioneers in simulation reviews of biomacromolecules.

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Additional resources for Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics

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2. Calculation of the structures of complexes with a flexible enzyme. : Experimental identification of a theoretically predicted “left sided” binding mode for (GlcNAc)6 in the active site of lysozyme. : Structure of cellulose. 2. Low-energy crystalline arrangements. A. : Protein modeling and structure prediction with a reduced representation. Acta Biochim. Biol. : Coarse-graining of condensed phase and biomolecular symmetry. : Computer simulation of protein folding. : An approximate treatment of long range interactions in proteins.

Energy parameters in polypeptides. IV. Semiempirical molecular orbital calculations of conformational dependence of energy and partial charge in di- and tripeptides. J. Phys. Chem. : Refinement of protein confirmations using a macromolecular energy minimization procedure. J. Mol. Biol. : Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. J. Am. Chem. Soc. : Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids.

The actual formulation of these potentials depends on how the main chain is represented in the model. In the cases where all backbone atoms are available, Ramachandrantype energy maps are utilized. , between the ith and i+2nd Cα, usually denoted as R13, as well as on R14 32 M. Blaszczyk et al. and R15. Another choice is to define energy terms based on planar and dihedral angles between successive Cα atoms. CG force field is often completed by terms that mimic solvent-induced effects and long range electrostatics.

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