Coverart for item
The Resource Computational Methods for Understanding Riboswitches, edited by Shi-Jie Chen, Donald H. Burke-Aguero

Computational Methods for Understanding Riboswitches, edited by Shi-Jie Chen, Donald H. Burke-Aguero

Label
Computational Methods for Understanding Riboswitches
Title
Computational Methods for Understanding Riboswitches
Statement of responsibility
edited by Shi-Jie Chen, Donald H. Burke-Aguero
Contributor
Editor
Subject
Language
eng
Summary
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
Member of
Cataloging source
E7B
Dewey number
572.8833
Illustrations
  • illustrations
  • plates
Index
index present
Language note
Text in English
LC call number
QP623
LC item number
.M484 2015eb
Literary form
non fiction
Nature of contents
  • dictionaries
  • bibliography
http://library.link/vocab/relatedWorkOrContributorName
  • Chen, Shi-Jie
  • Burke, Donald H.
Series statement
Methods in enzymology,
Series volume
v. 553
http://library.link/vocab/subjectName
  • RNA
  • Riboswitches
  • Enzymes
  • Riboswitch
  • Nucleic Acids
  • SCIENCE
  • Enzymes
  • Riboswitches
  • RNA
Label
Computational Methods for Understanding Riboswitches, edited by Shi-Jie Chen, Donald H. Burke-Aguero
Instantiates
Publication
Copyright
Bibliography note
Includes bibliographical references at the end of each chapters and indexes
Carrier category
online resource
Carrier category code
  • cr
Carrier MARC source
rdacarrier
Color
multicolored
Content category
text
Content type code
  • txt
Content type MARC source
rdacontent
Contents
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
Control code
905867773
Dimensions
unknown
Edition
First edition.
Extent
1 online resource (xvii, 403 pages, 26 unnumbered pages of plates)
Form of item
online
Isbn
9780128016183
Media category
computer
Media MARC source
rdamedia
Media type code
  • c
Other physical details
color illustrations.
http://library.link/vocab/ext/overdrive/overdriveId
785308
Specific material designation
remote
System control number
(OCoLC)905867773
Label
Computational Methods for Understanding Riboswitches, edited by Shi-Jie Chen, Donald H. Burke-Aguero
Publication
Copyright
Bibliography note
Includes bibliographical references at the end of each chapters and indexes
Carrier category
online resource
Carrier category code
  • cr
Carrier MARC source
rdacarrier
Color
multicolored
Content category
text
Content type code
  • txt
Content type MARC source
rdacontent
Contents
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
Control code
905867773
Dimensions
unknown
Edition
First edition.
Extent
1 online resource (xvii, 403 pages, 26 unnumbered pages of plates)
Form of item
online
Isbn
9780128016183
Media category
computer
Media MARC source
rdamedia
Media type code
  • c
Other physical details
color illustrations.
http://library.link/vocab/ext/overdrive/overdriveId
785308
Specific material designation
remote
System control number
(OCoLC)905867773

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