Multiscale Approaches to Protein Modeling

by Andrzej Kolinski (Editor)

Overview

The book gives a comprehensive review of the most advanced multiscale methods for protein structure prediction, computational studies of protein dynamics, folding mechanisms and macromolecular interactions. It approaches span a wide range of the levels of coarse-grained representations, various sampling techniques and variety of applications to biomedical and biophysical problems. This book is intended to be used as a reference book for those who are just beginning their adventure with biomacromolecular modeling but also as a valuable source of detailed information for those who are already experts in the field of biomacromolecular modeling and in related areas of computational biology or biophysics.

Product Details

ISBN-13:	9781441968883
Publisher:	Springer New York
Publication date:	10/15/2010
Edition description:	2011
Pages:	355
Product dimensions:	6.30(w) x 9.30(h) x 1.10(d)

Table of Contents

1 Lattice Polymers and Protein Models Andrzej Kolinski 1

2 Multiscale Protein and Peptide Docking Mateusz Kurcinski Michal Jamroz Andrzej Kolinski 21

3 Coarse-Grained Models of Proteins: Theory and Applications Cezary Czaplewski Adam Liwo Mariusz Makowski Stanislaw Oldziej Harold A. Scheraga 35

4 Conformational Sampling in Structure Prediction and Refinement with Atomistic and Coarse-Gained Models Michael Feig Srinivasa M. Gopal Kanagasabai Vadivel Andrew Stumpff-Kane 85

5 Effective All-Atom Potentials for Proteins Anders Iibäck Sandipan Mohanty 111

6 Statistical Contact Potentials in Protein Coarse-Grained Modeling: From Pair to Multi-body Potentials Sumudu P. Leelananda Yaping Feng Pawel Gniewek Andrzej Kloczkowski Robert L. Jernigan 127

7 Bridging the Atomic and Coarse-Grained Descriptions of Collective Motions in Proteins Vincenzo Carnevale Cristian Micheletti Francesco Pontiggia Raffaello Potestio 159

8 Structure-Based Models of Biomolecules: Stretching of Proteins, Dynamics of Knots, Hydrodynamic Effects, and Indentation of Virus Capsids Marek Cieplak Joanna I. Sulkowska 179

9 Sampling Protein Energy Landscapes - The Quest for Efficient Algorithms Ulrich H. E. Hansmann 209

10 Protein Structure Prediction: From Recognition of Matches with Known Structures to Recombination of Fragments Michal J. Gajda Marcin Pawlowski Janusz M. Bujnicki 231

11 Genome-Wide Protein Structure Prediction Srayanta Mukherjee Andras Szilagyi Ambrish Roy Yang Zhang 255

12 Multiscale Approach to Protein Folding Dynamics Sebastian Kmiecik Michal Jamroz Andrzej Kolinski 281

13 Error Estimation of Template-Based Protein Structure Models Daisuke Kihara Yifeng David Yang Hao Chen 295

14 Evaluation of Protein Structure Prediction Methods: Issues and Strategics Anna Tramontano Domenico Cozzetto 315

Index 341