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 Prediction1. Automated 3D RNA Structure Prediction Using the RNAComposer Method for RiboswitchesK. J. Purzycka, M. Popenda, M. Szachniuk,  M. Antczak, P. Lukasiak, J. Blazewicz and R.W. Adamiak2. Modeling Complex RNA Tertiary Folds with RosettaClarence Yu Cheng, Fang-Chieh Chou and Rhiju Das3. Computational Methods Toward Accurate RNA Structure Prediction Using Coarse-Grained and All-Atom ModelsAndrey Krokhotin and Nikolay V. Dokholyan 4. Improving RNA Secondary Structure Prediction with Structure Mapping DataMichael F. Sloma and David H. Mathews5. Computational Prediction of Riboswitch Tertiary Structures including Pseudoknots by RAGTOP: A Hierarchical Graph Sampling ApproachNamhee Kim, Mai Zahran and Tamar SchlickPart II. RNA Dynamics and Thermodynamics6. Using Reweighted Pulling Simulations to Characterize Conformational Changes in RiboswitchesFrancesco Di Palma, Francesco Colizzi and Giovanni Bussi7. Force Field Dependence of Riboswitch DynamicsChristian A. Hanke and Holger Gohlke8. Thermodynamic and Kinetic Folding of RiboswitchesStefan Badelt, Stefan Hammer, Christoph Flamm and Ivo L. Hofacker9. Integrating Molecular Dynamics Simulations with Chemical Probing Experiments using SHAPE-FITSerdal Kirmizialtin, Scott P. Hennelly, Alexander Schug, Jose N. Onuchic and Karissa Y. Sanbonmatsu10. Using Simulations and Kinetic Network Models to Reveal the Dynamics and Functions of RiboswitchesJong-Chin Lin, Jeseong Yoon, Changbong Hyeon and D. ThirumalaiPart III. Ions, Ligands, and RNA Interactions11. Computational Methods for Prediction of RNA Interactions with Metal Ions and Small Organic LigandsAnna Philips, Grzegorz Łach and Janusz M. Bujnicki12. Computational Prediction of RiboswitchesP. Clote13. Computational and Experimental Studies of Reassociating RNA/DNA Hybrids Containing Split FunctionalitiesKirill A. Afonin, Eckart Bindewald, Maria Kireeva and Bruce A. Shapiro14. Multiscale Methods for Computational RNA EnzymologyMaria T. Panteva, Thakshila Dissanayake, Haoyuan Chen, Brian K. Radak, Erich R. Kuechler, George M. Giambasu, Tai-Sung Lee and Darrin M. York

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