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

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

Since the second one half the twentieth century laptop computations have performed a severe position in technology and engineering. Computer-based recommendations became specifically very important in molecular biology, due to the fact they generally signify the single attainable method to achieve insights into the habit of a organic procedure as an entire. The complexity of organic platforms, which generally should be analyzed on assorted time- and size-scales and with diversified degrees of accuracy, calls for the appliance of other methods, starting from comparative research of sequences and structural databases, to the research of networks of interdependence among phone elements and methods, via coarse-grained modeling to atomically precise simulations, and at last to molecular quantum mechanics.

This ebook presents a entire assessment of recent computer-based thoughts for computing the constitution, houses and dynamics of biomolecules and biomolecular methods. The twenty-two chapters, written by means of scientists from worldwide, tackle the speculation and perform of computing device simulation recommendations within the learn of organic phenomena. The chapters are grouped into 4 thematic sections facing the next issues: the technique of molecular simulations; functions of molecular simulations; bioinformatics tools and use of experimental details in molecular simulations; and chosen functions of molecular quantum mechanics. The publication comprises an introductory bankruptcy written through Harold A. Scheraga, one of many actual 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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1997) which turned out to be the most effective. Later, UNRES was extended to mesoscopic Molecular Dynamics (MD) to study pathways and kinetics of the protein folding process. This implementation of MD reformulates the conformational sampling as a search for the most probable conformational ensembles with the lowest free energy at temperatures below the folding transition temperature. The UNRES Coarse-Grained Protein Models in Structure Prediction 37 extension of MD can also be used to simulate multichain proteins.

Phys. Lett. : Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA and CFMC. J. Comput. Chem. : Multiplexed-Replica Exchange Molecular Dynamics Method for Protein Folding Simulation. Biophys. J. : Application of multiplexed replica exchange molecular dynamics to the UNRES force field: tests with α and α + β proteins. J. Chem. Theory and Comput. : Mechanism of fiber assembly; treatment of Aβ-peptide aggregation with a coarse-grained united-residue force field.

Chem. : Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 3. Use of many proteins in optimization. J Phys. Chem. : Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc. Natl. Acad. Sci. : Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode. J. Phys. Chem. : Molecular dynamics with the united-residue model of polypeptide chains.

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