Computational Methods Developed for Understanding RNA Structure

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 dynamicsContains chapters with emerging topics such as RNA structure prediction, riboswitch dynamics and thermodynamics, and effects of ions and ligands. INDICE: I. RNA Structure Prediction1. Automated 3D RNA structure prediction using the RNAComposer method for riboswitches  Ryszard W. Adamiak2. Medium-resolution 3D modeling of riboswitch domains with fragment assembly of RNA  Rhiju Das3. Towards accurate RNA-structure prediction using coarse-grained and all-atom models  Nikolay Dokholyan4. Integration of RNA 3D structural and sequence data for gene and structure prediction  Neocles Leontis5. Improving RNA secondary structure modeling with experimental mapping data  David Matthews6. Computational prediction of riboswitch tertiary structures by a graph modeling approach  Tamar SchlickII. RNA Dynamics and Thermodynamics7. Using atomistic molecular dynamics and enhanced sampling techniques to characterize the adenine riboswitch folding mechanism  Giovanni Bussi8. Molecular dynamics simulations of riboswitches using the Amber force field - avoiding pitfalls  Holger Gohlke9. Thermodynamic and kinetic folding of riboswitches  Ivo Hofacker10. Modeling the dynamics of riboswitches at the secondary structure level  Francois Major11. Integrating molecular simulations with chemical probing experiments using MD-SHAPE  Karissa Sanbonmatsu12. Using coarse-Grained simulations to understand functions of riboswitches  Devarajan ThirumalaiIII. Ions, Ligands, and RNA Interactions13. Computational methods for prediction of RNA interactions with ions and small molecule ligands  Janusz M. Bujnicki14. Molecular dynamics simulations on Mg2+ dependent loop structure  Thomas E. Cheatham15. Bioinformatics of riboswitches  Peter Clote16. Computational and experimental studies of re-associating RNA/DNA hybrids containing split functionalities  Bruce A. Shapiro17. Mechanisms of catalytic riboswitches studied with multiscale quantum simulations  Darrin York

• ISBN: 978-0-12-801429-5
• Editorial: Academic Press
• Encuadernacion: Cartoné
• Páginas: 412
• Fecha Publicación: 01/02/2015
• Nº Volúmenes: 1
• Idioma: Inglés