Coarse-Grained Modeling of Biomolecules

✍ Scribed by Garegin A. Papoian

• Publisher: CRC Press
• Year: 2018
• Tongue: English
• Leaves: 459
• Series: Series in Computational Biophysics
• Edition: 1
• Category: Library

✦ Synopsis

"The chapters in this book survey the progress in simulating biomolecular dynamics…. The images conjured up by this work are not yet universally loved, but are beginning to bring new insights into the study of biological structure and function. The future will decide whether this scientific movement can bring forth its Picasso or Modigliani." –from the Foreword by Peter G. Wolynes, Bullard-Welch Foundation Professor of Science, Rice University

This book highlights the state-of-art in coarse-grained modeling of biomolecules, covering both fundamentals as well as various cutting edge applications. Coarse-graining of biomolecules is an area of rapid advances, with numerous new force fields having appeared recently and significant progress made in developing a systematic theory of coarse-graining. The contents start with first fundamental principles based on physics, then survey specific state-of-art coarse-grained force fields of proteins and nucleic acids, and provide examples of exciting biological problems that are at large scale, and hence, only amenable to coarse-grained modeling.

• Introduces coarse-grained models of proteins and nucleic acids.
• Showcases applications such as genome packaging in nuclei and understanding ribosome dynamics
• Gives the physical foundations of coarse-graining
• Demonstrates use of models for large-scale assemblies in modern studies

Garegin A. Papoian is the first Monroe Martin Associate Professor with appointments in the Department of Chemistry and Biochemistry and the Institute for Physical Science and Technology at the University of Maryland.

✦ Table of Contents

Content: Inverse Monte Carlo methods / Alexander P. Lyubartsev --
Thermodynamically consistent coarse-graining of polymers / Marina G. Guenza --
Microscopic physics-based models of proteins and nucleic acids: UNRES and NARES / Maciej Baranowski, Cezary Czaplewski, Ewa I. Gołaś, Yuan-Jie He, Dawid Jagieła, Paweł Krupa, Adam Liwo, Gia G. Maisuradze, Mariusz Makowski, Magdalena A. Mozolewska, Andrei Niadzvedtski, Antti J. Niemi, Shelly Rackovsky, Rafał Ślusarz, Adam K. Sieradzan, Stanisław Ołdziej, Tomas Wirecki, Yanping Yin, Bartłomiej Zaborowski, and Harold A. Scheraga --
AWSEM-MD: predicting protein structure and function / Garegin A. Papoian and Peter G. Wolynes --
Elastic models of biomolecules / Qiang Cui --
Knowledge-based models: RNA / Raúl Méndez, Andrey Krokhotin, Marino Convertino, Jhuma Das, Arpit Tandon, Nikolay V. Dokholyan --
The need for computational speed: state of the art in DNA coarse graining / Davit Potoian and Garegin A. Papoian --
Coarse-grained modeling of nucleosomes and chromatin / Lars Nordenskiöld, Alexander P. Lyubartsev, and Nikolay Korolev --
Modeling of genomes / Naoko Tokuda and Masaki Sasai --
Mechanics of viruses / Olga Kononova, Artem Zhmurov, Kenneth A. Marx and Valeri Barsegov.

✦ Subjects

Biomolecules -- Models.