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 half the twentieth century computing device computations have performed a severe function in technological know-how and engineering. Computer-based recommendations became specifically very important in molecular biology, considering the fact that they generally signify the one attainable method to achieve insights into the habit of a organic approach as an entire. The complexity of organic platforms, which typically has to be analyzed on varied time- and size-scales and with diverse degrees of accuracy, calls for the applying of other methods, starting from comparative research of sequences and structural databases, to the research of networks of interdependence among telephone elements and tactics, via coarse-grained modeling to atomically special simulations, and at last to molecular quantum mechanics.

This e-book presents a complete evaluate of contemporary computer-based concepts for computing the constitution, homes and dynamics of biomolecules and biomolecular tactics. The twenty-two chapters, written by means of scientists from world wide, deal with the speculation and perform of laptop simulation suggestions within the learn of organic phenomena. The chapters are grouped into 4 thematic sections facing the subsequent issues: the technique of molecular simulations; functions of molecular simulations; bioinformatics equipment and use of experimental details in molecular simulations; and chosen functions of molecular quantum mechanics. The publication contains an introductory bankruptcy written through Harold A. Scheraga, one of many real pioneers in simulation experiences 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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J. Phys. Chem. : Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues. J. Chem. : Prediction of protein conformation on the basis of a search for compact structures; test on avian pancreatic polypeptide. : A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data. J. Comput. Chem. : A united-residue force field for off-lattice protein-structure simulations.

Sci. : Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state. Proc. Natl. Acad. Sci. 109, 10346–10351 (2012) [150] Schlick, T. ): Innovations in Biomolecular Modeling and Simulations, vols. 1 and 2. Royal Society of Chemistry, Cambridge (2012) Coarse-Grained Protein Models in Structure Prediction Maciej Blaszczyk, Dominik Gront, Sebastian Kmiecik, Katarzyna Ziolkowska, Marta Panek, and Andrzej Kolinski* Abstract. The knowledge of the three-dimensional structure of proteins is crucial for understanding many important biological processes.

2009; Kolinski 2004; Liwo et al. 2001). Another very important energy component is the one corresponding to hard core repulsion between atoms, often described as an excluded volume term. , a polynomial of a high order (order of 12 corresponds to the Lennard-Jones potential). Relevant radii for united atoms are computed as an average over all the relevant conformations of a group that has been coarse grained into a sphere. Hard core repulsion in low- to medium-resolution on-lattice models may be evaluated instantly just by a single look-up in the 3D matrix that stores the lattice space.

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