Full Description
This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers computational prediction RNA structure and dynamics, including such topics as computational modeling of RNA secondary and tertiary structures, riboswitch dynamics, and ion-RNA, ligand-RNA and DNA-RNA interactions.
Contents
Part I. RNA Structure Prediction
1. 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
2. Modeling Complex RNA Tertiary Folds with Rosetta
Clarence Yu Cheng, Fang-Chieh Chou and Rhiju Das
3. Computational Methods Toward Accurate RNA Structure Prediction Using Coarse-Grained and All-Atom Models
Andrey Krokhotin and Nikolay V. Dokholyan
4. Improving RNA Secondary Structure Prediction with Structure Mapping Data
Michael F. Sloma and David H. Mathews
5. Computational Prediction of Riboswitch Tertiary Structures including Pseudoknots by RAGTOP: A Hierarchical Graph Sampling Approach
Namhee Kim, Mai Zahran and Tamar Schlick
Part II. RNA Dynamics and Thermodynamics
6. Using Reweighted Pulling Simulations to Characterize Conformational Changes in Riboswitches
Francesco Di Palma, Francesco Colizzi and Giovanni Bussi
7. Force Field Dependence of Riboswitch Dynamics
Christian A. Hanke and Holger Gohlke
8. Thermodynamic and Kinetic Folding of Riboswitches
Stefan Badelt, Stefan Hammer, Christoph Flamm and Ivo L. Hofacker
9. 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
10. Using Simulations and Kinetic Network Models to Reveal the Dynamics and Functions of Riboswitches
Jong-Chin Lin, Jeseong Yoon, Changbong Hyeon and D. Thirumalai
Part III. Ions, Ligands, and RNA Interactions
11. Computational Methods for Prediction of RNA Interactions with Metal Ions and Small Organic Ligands
Anna Philips, Grzegorz Łach and Janusz M. Bujnicki
12. Computational Prediction of Riboswitches
P. Clote
13. Computational and Experimental Studies of Reassociating RNA/DNA Hybrids Containing Split Functionalities
Kirill A. Afonin, Eckart Bindewald, Maria Kireeva and Bruce A. Shapiro
14. Multiscale Methods for Computational RNA Enzymology
Maria T. Panteva, Thakshila Dissanayake, Haoyuan Chen, Brian K. Radak, Erich R. Kuechler, George M. Giambasu, Tai-Sung Lee and Darrin M. York
