Computational Methods for Understanding Riboswitches

<p>Part I. RNA Structure Prediction<br>1. Automated 3D RNA Structure Prediction Using the RNAComposer Method for Riboswitches<br>K. J. Purzycka, M. Popenda, M. Szachniuk,  M. Antczak, P. Lukasiak, J. Blazewicz and R.W. Adamiak<br>2. Modeling Complex RNA Tertiary Folds with Rosetta<br>Clarence Yu Cheng, Fang-Chieh Chou and Rhiju Das<br>3. Computational Methods Toward Accurate RNA Structure Prediction Using Coarse-Grained and All-Atom Models<br>Andrey Krokhotin and Nikolay V. Dokholyan <br>4. Improving RNA Secondary Structure Prediction with Structure Mapping Data<br>Michael F. Sloma and David H. Mathews<br>5. Computational Prediction of Riboswitch Tertiary Structures including Pseudoknots by RAGTOP: A Hierarchical Graph Sampling Approach<br>Namhee Kim, Mai Zahran and Tamar Schlick</p> <p>Part II. RNA Dynamics and Thermodynamics<br>6. Using Reweighted Pulling Simulations to Characterize Conformational Changes in Riboswitches<br>Francesco Di Palma, Francesco Colizzi and Giovanni Bussi<br>7. Force Field Dependence of Riboswitch Dynamics<br>Christian A. Hanke and Holger Gohlke<br>8. Thermodynamic and Kinetic Folding of Riboswitches<br>Stefan Badelt, Stefan Hammer, Christoph Flamm and Ivo L. Hofacker<br>9. Integrating Molecular Dynamics Simulations with Chemical Probing Experiments using SHAPE-FIT<br>Serdal Kirmizialtin, Scott P. Hennelly, Alexander Schug, Jose N. Onuchic and Karissa Y. Sanbonmatsu<br>10. Using Simulations and Kinetic Network Models to Reveal the Dynamics and Functions of Riboswitches<br>Jong-Chin Lin, Jeseong Yoon, Changbong Hyeon and D. Thirumalai</p> <p>Part III. Ions, Ligands, and RNA Interactions<br>11. Computational Methods for Prediction of RNA Interactions with Metal Ions and Small Organic Ligands<br>Anna Philips, Grzegorz Łach and Janusz M. Bujnicki<br>12. Computational Prediction of Riboswitches<br>P. Clote<br>13. Computational and Experimental Studies of Reassociating RNA/DNA Hybrids Containing Split Functionalities<br>Kirill A. Afonin, Eckart Bindewald, Maria Kireeva and Bruce A. Shapiro<br>14. Multiscale Methods for Computational RNA Enzymology<br>Maria T. Panteva, Thakshila Dissanayake, Haoyuan Chen, Brian K. Radak, Erich R. Kuechler, George M. Giambasu, Tai-Sung Lee and Darrin M. York<br></p>