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Computational Methods for Understanding Riboswitches /
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 structure...
| Clasificación: | Libro Electrónico |
|---|---|
| Otros Autores: | , |
| Formato: | Electrónico eBook |
| Idioma: | Inglés |
| Publicado: |
Waltham, Massachusetts :
Academic Press,
2015.
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| Edición: | First edition. |
| Colección: | Methods in enzymology ;
v. 553. |
| Temas: | |
| Acceso en línea: | Texto completo Texto completo |
Tabla de Contenidos:
- Section I. RNA structure prediction. 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 ; Modeling complex RNA tertiary folds with Rosetta / Clarence Yu Cheng, Fang-Chieh Chou, and Rhiju Das ; Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models / Andrey Krokhotin and Nikolay V. Dokholyan ; Improving RNA secondary structure prediction with structure mapping data / Michael F. Sloma and David H. Mathews ; Computational prediction of riboswitch tertiary structures including pseudoknots by RAGTOP : a hierarchical graph sampling approach / Namhee Kim, Mai Zahran, and Tamar Schlick
- Section II. RNA dynamics and thermodynamics. Using reweighted pulling simulations to characterize conformational changes in riboswitches / Francesco Di Palma, Francesco Colizzi, and Giovanni Bussi ; Force field dependence of riboswitch dynamics / Christian A. Hanke and Holger Gohlke ; Thermodynamic and kinetic folding of riboswitches / Stefan Badelt, Stefan Hammer, Christoph Flamm, and Ivo L. Hofacker ; 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 ; Using simulations and kinetic network models to reveal the dynamics and functions of riboswitches / Jong-Chin Lin, Jeseong Yoon, Changbong Hyeon, and D. Thirumalai
- Section III. Ions, ligands, and RNA interactions. Computational methods for prediction of RNA interactions with metal ions and small organic ligands / Anna Philips, Grzegorz �ach, and Janusz M. Bujnicki ; Computational prediction of riboswitches / P. Clote ; Computational and experimental studies of reassociating RNA/DNA hybrids containing split functionalities / Kirill A. Afonin, Eckart Bindewald, Maria Kireeva, and Bruce A. Shapiro ; Multiscale methods for computational RNA enzymology / Maria T. Panteva, Thakshila Dissanayake, Haoyuan Chen, Brian K. Radak, Erich R. Kuechler, George M. Giamba�su, Tai-Sung Lee, and Darrin M. York.