00000nmm a2200000 i 4500 UP-1685506469195176345 Buklod 20230510150053.0 m o u cr ||||||||||| 230412t20152015mau u eng d 9780128014295 (OCoLC)905651450 OCLCQ DSCI rda eng QP 623.5 M47 C66 2015eb Computational methods for understanding riboswitches edited by Shi-Jie Chen, Donald H. Burke-Aguero. Waltham, MA Elsevier/Academic Press [2015] 1 online resource (xvii, 403 pages, 26 unnumbered pages of plates) illustrations text rdacontent computer rdamedia online resource rdacarrier Methods in enzymology volume 553 Includes bibliographical references and indexes 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. Giambaðsu, Tai-Sung Lee, and Darrin M. Yo IP-based subscription, on campus only. Access via Electronic Resources of the UPD University Library Website. Riboswitches Computer simulation. Messenger RNA Computer simulation. Riboswitch. Computational biology Methods. Electronic books. Chen, Shi-Jie editor. Burke, Donald H. editor. Methods in enzymology volume 553. Available for University of the Philippines System via Science Direct. Also available remotely for University of the Philippines System via Science Direct through. Click here to access thru Open Athens: https://www.sciencedirect.com/bookseries/methods-in-enzymology/vol/553/suppl/C (viewed 12 April 2023) FO UPD DSCI Electronic Resource