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Multiscale Approaches to Protein Modeling

Structure Prediction, Dynamics, Thermodynamics and Macromolecular Assemblies

  • Andrzej Kolinski

Table of contents

  1. Front Matter
    Pages i-xii
  2. Andrzej Kolinski
    Pages 1-20
  3. Mateusz Kurcinski, Michał Jamroz, Andrzej Kolinski
    Pages 21-33
  4. Cezary Czaplewski, Adam Liwo, Mariusz Makowski, Stanisław Ołdziej, Harold A. Scheraga
    Pages 35-83
  5. Michael Feig, Srinivasa M. Gopal, Kanagasabai Vadivel, Andrew Stumpff-Kane
    Pages 85-109
  6. Anders Irbäck, Sandipan Mohanty
    Pages 111-126
  7. Sumudu P. Leelananda, Yaping Feng, Pawel Gniewek, Andrzej Kloczkowski, Robert L. Jernigan
    Pages 127-157
  8. Vincenzo Carnevale, Cristian Micheletti, Francesco Pontiggia, Raffaello Potestio
    Pages 159-178
  9. Srayanta Mukherjee, Andras Szilagyi, Ambrish Roy, Yang Zhang
    Pages 255-279
  10. Sebastian Kmiecik, Michał Jamroz, Andrzej Kolinski
    Pages 281-293
  11. Daisuke Kihara, Yifeng David Yang, Hao Chen
    Pages 295-314
  12. Anna Tramontano, Domenico Cozzetto
    Pages 315-339
  13. Back Matter
    Pages 341-355

About this book

Introduction

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 “brute 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.

Editors and affiliations

  • Andrzej Kolinski
    • 1
  1. 1.Dept. ChemistryUniversity of WarsawWarszawaPoland

Bibliographic information