Computational methods for understanding riboswitches / edited by Shi-Jie Chen, Donald H. Burke-Aguero.

Format:

Book

Contributor:

Chen, Shi-Jie, editor.

Burke, Donald H., editor.

Series:

Methods in enzymology ; v. 553.

Methods in enzymology, 0076-6879 ; volume 553

Language:

English

Subjects (All):

Riboswitches--Computer simulation.

Riboswitches.

Messenger RNA--Computer simulation.

Messenger RNA.

RNA.

Computer simulation.

Physical Description:

xvii, 403 pages, 26 unnumbered pages of plates : illustrations ; 24 cm.

Edition:

First edition.

Place of Publication:

Amsterdam ; Boston : Elsevier/Academic Press, 2015.

Contents:

Section I. RNA structure prediction. Automated 3D RNA structure prediction using the RNAComposer method for riboswitches / K.J. Purzycka, M. Popenda, M. Szachniuk, M. Antczak, P. Lukasiak, J. Blazewicz, and R.W. Adamiak ; Modeling complex RNA tertiary folds with Rosetta / Clarence Yu Cheng, Fang-Chieh Chou, and Rhiju Das ; Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models / Andrey Krokhotin and Nikolay V. Dokholyan ; Improving RNA secondary structure prediction with structure mapping data / Michael F. Sloma and David H. Mathews ; Computational prediction of riboswitch tertiary structures including pseudoknots by RAGTOP : a hierarchical graph sampling approach / Namhee Kim, Mai Zahran, and Tamar Schlick

Section II. RNA dynamics and thermodynamics. Using reweighted pulling simulations to characterize conformational changes in riboswitches / Francesco Di Palma, Francesco Colizzi, and Giovanni Bussi ; Force field dependence of riboswitch dynamics / Christian A. Hanke and Holger Gohlke ; Thermodynamic and kinetic folding of riboswitches / Stefan Badelt, Stefan Hammer, Christoph Flamm, and Ivo L. Hofacker ; Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT / Serdal Kirmizialtin, Scott P. Hennelly, Alexander Schug, Jose N. Onuchic, and Karissa Y. Sanbonmatsu ; Using simulations and kinetic network models to reveal the dynamics and functions of riboswitches / Jong-Chin Lin, Jeseong Yoon, Changbong Hyeon, and D. Thirumalai

Section III. Ions, ligands, and RNA interactions. Computational methods for prediction of RNA interactions with metal ions and small organic ligands / Anna Philips, Grzegorz Łach, and Janusz M. Bujnicki ; Computational prediction of riboswitches / P. Clote ; Computational and experimental studies of reassociating RNA/DNA hybrids containing split functionalities / Kirill A. Afonin, Eckart Bindewald, Maria Kireeva, and Bruce A. Shapiro ; Multiscale methods for computational RNA enzymology / Maria T. Panteva, Thakshila Dissanayake, Haoyuan Chen, Brian K. Radak, Erich R. Kuechler, George M. Giambaşu, Tai-Sung Lee, and Darrin M. York.

Notes:

Includes bibliographical references and indexes.

ISBN:

9780128014295

0128014296

OCLC:

905651450