Computational Methods for Understanding Riboswitches / edited by Shi-Jie Chen, Donald H. Burke-Aguero.
Contributor(s): Chen, Shi-Jie [editor.] | Burke, Donald H [editor.]Material type: TextSeries: Methods in enzymology: v. 553.Publisher: Waltham, Massachusetts : Academic Press, 2015Copyright date: ©2015Edition: First editionDescription: 1 online resource (xvii, 403 pages, 26 unnumbered pages of plates) : color illustrationsContent type: text Media type: computer Carrier type: online resourceISBN: 9780128016183; 0128016183Subject(s): RNA | Riboswitches | Enzymes | SCIENCE -- Life Sciences -- Biochemistry | Enzymes | Riboswitches | RNA | Riboswitch | Nucleic AcidsGenre/Form: Electronic books. Additional physical formats: Print version:: Methods in enzymology : computational methods for understanding riboswitches.DDC classification: 572.8833 LOC classification: QP623 | .M484 2015ebOnline resources: Click here to access online
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Text in English.
Includes bibliographical references at the end of each chapters 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 Łach, 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. Giambaşu, Tai-Sung Lee, and Darrin M. York.
Online resource; title from PDF title page (ebrary, viewed March 5, 2015).
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 structures, riboswitch dynamics, and ion-RNA, ligand-RNA and DNA-RNA interactions. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers computational methods and applications in RNA structure and dynamics.