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.
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 Lach 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