Computational Methods for Understanding Riboswitches

Shi-Jie Chen is Professor of the Department of Physics Astronomy and Department of Biochemistry and is core faculty member in the Informatics Institute at the University of Missouri-Columbia. Dr. Chen received his Ph.D. in Physics from the University of California, San Diego in 1994. He was a postdoctoral researcher at the University of California, San Francisco in 1994-9 and began his faculty appointment at the University of Missouri-Columbia in 1999. Chen has served the scientific community by his participation on multiple NIH review panels and site visit reviewer teams. He served as Associate Editor of the PLoS Computational Biology. His laboratory developed Vfold and TBI, open source and freely available web servers and software for the computational predictions of RNA structure, folding thermodynamics, and ion effects. Dr. Chen was elected to the fellow of American Physical Society in 2012.

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