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Multiscale Approaches to Protein Modeling: Structure Prediction, Dynamics, Thermodynamics and Macromolecular Assemblies

✍ Scribed by Andrzej Kolinski (auth.), Andrzej Kolinski (eds.)


Publisher
Springer-Verlag New York
Year
2011
Tongue
English
Leaves
368
Edition
1
Category
Library

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✦ Synopsis


Multiscale Approaches to Protein Modeling is a comprehensive review of the most advanced multiscale methods for protein structure prediction, computational studies of protein dynamics, folding mechanisms and macromolecular interactions. The approaches span a wide range of the levels of coarse-grained representations, various sampling techniques and variety of applications to biomedical and biophysical problems. Thanks to enormous progress in sequencing of genomic data, we presently know millions of protein sequences. At the same time, the number of experimentally solved protein structures is much smaller, ca. 60,000. This is because of the large cost of structure determination. Thus, theoretical, in silico, prediction of protein structures and dynamics is essential for understanding the molecular basis of drug action, metabolic and signaling pathways in living cells, designing new technologies in the life science and material sciences. Unfortunately, a β€œbrute force” approach remains impractical. Folding of a typical protein (in vivo or in vitro) takes milliseconds to minutes, while state-of-the-art all-atom molecular mechanics simulations of protein systems can cover only a time period range of nanosecond to microseconds. This is the reason for the enormous progress in development of various mutiscale modeling techniques, applied to protein structure prediction, modeling of protein dynamics and folding pathways, in silico protein engineering, model-aided interpretation of experimental data, modeling of macromolecular assemblies and theoretical studies of protein thermodynamics. Coarse-graining of the proteins’ conformational space is a common feature of all these approaches, although the details and the underlying physical models span a very broad spectrum.

✦ Table of Contents


Front Matter....Pages i-xii
Lattice Polymers and Protein Models....Pages 1-20
Multiscale Protein and Peptide Docking....Pages 21-33
Coarse-Grained Models of Proteins: Theory and Applications....Pages 35-83
Conformational Sampling in Structure Prediction and Refinement with Atomistic and Coarse-Grained Models....Pages 85-109
Effective All-Atom Potentials for Proteins....Pages 111-126
Statistical Contact Potentials in Protein Coarse-Grained Modeling: From Pair to Multi-body Potentials....Pages 127-157
Bridging the Atomic and Coarse-Grained Descriptions of Collective Motions in Proteins....Pages 159-178
Structure-Based Models of Biomolecules: Stretching of Proteins, Dynamics of Knots, Hydrodynamic Effects, and Indentation of Virus Capsids....Pages 179-208
Sampling Protein Energy Landscapes – The Quest for Efficient Algorithms....Pages 209-230
Protein Structure Prediction: From Recognition of Matches with Known Structures to Recombination of Fragments....Pages 231-254
Genome-Wide Protein Structure Prediction....Pages 255-279
Multiscale Approach to Protein Folding Dynamics....Pages 281-293
Error Estimation of Template-Based Protein Structure Models....Pages 295-314
Evaluation of Protein Structure Prediction Methods: Issues and Strategies....Pages 315-339
Back Matter....Pages 341-355

✦ Subjects


Protein Science; Protein Structure; Bioinformatics; Computational Biology/Bioinformatics


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