Format:
Online-Ressource (PDF-Dateien, XVII, 403 S.)
Edition:
Online-Ausg.
ISBN:
9780128014295
,
0128016183
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9780128016183
Series Statement:
Methods in enzymology 553
Content:
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.
Note:
Description based upon print version of record
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Front Cover; Computational Methods for Understanding Riboswitches; Copyright; Contents; Contributors; Preface; Section I: RNA Structure Prediction; Chapter 1: Automated 3D RNA Structure Prediction Using the RNAComposer Method for Riboswitches1; 1. Introduction; 2. RNA FRABASE-Opening the Route to RNAComposer; 3. RNAComposer-From the RNA Secondary Structure to RNA 3D Structure; 3.1. General description of the RNAComposer method; 3.2. RNAComposer input data; 3.3. Output data and quality control of the 3D models; 3.3.1. RNApdbee-Application in the RNA 3D structure validation
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3.3.2. RNAlyzer-New tool for the 3D structure quality assessment3.4. RNAComposer web server; 4. Predicting the Tertiary Structure of Riboswitches with RNAComposer; 4.1. RNAComposer accurately predicts 3D structure of several complex riboswitches; 4.2. Application example 1: The c-di-GMP-II riboswitch; 4.3. Application example 2: The c-di-GMP-II riboswitch relatives; 5. Conclusions and Perspectives; Acknowledgments; References; Chapter 2: Modeling Complex RNA Tertiary Folds with Rosetta; 1. Introduction; 2. Setting the Stage for 3D Modeling Using Experimental Data
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3. Making Models of RNA Tertiary Folds3.1. Installing software and accessing computation resources; 3.2. Preassembling helices; 3.3. Defining the global fold using fragment assembly of RNA; 3.4. Producing and selecting models with reasonable stereochemistry using refinement; 3.5. Clustering to generate final set of models; 3.6. Advanced strategies: Building subpieces into existing models; 4. Evaluation; 5. Conclusion; Acknowledgments; Appendix. Example Command Lines and Files for RNA Modeling in Rosetta; References
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Chapter 3: Computational Methods Toward Accurate RNA Structure Prediction Using Coarse-Grained and All-Atom Models1. Introduction; 2. Discrete Molecular Dynamics; 3. Three-Bead Model; 3.1. Model geometry and interaction potential; 3.1.1. Base-pairing; 3.1.2. Phosphate repulsion; 3.1.3. Hydrophobic interactions; 3.1.4. Base stacking; 3.1.5. Parameterization of the hydrogen-bond, base-stacking, and hydrophobic interactions; 3.1.6. Loop entropy; 3.2. Prediction of small RNA structure; 4. Use of Hydroxyl-Radical Probing to Refine RNA Three-Dimensional Structure
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4.1. Folding RNA with experimental constraints4.2. Definition of through-space contacts; 4.3. HRP bias potential; 4.4. Assignment of interaction parameters; 4.5. Simulation protocol; 4.6. Results, significance of predictions, and the scope of applicability of the method; 5. All-Atom Structure Reconstruction; 6. iFoldRNA; 7. Conclusions; References; Chapter 4: Improving RNA Secondary Structure Prediction with Structure Mapping Data; 1. Introduction; 2. Overview of Probing methods; 2.1. Overview; 2.2. Chemical probing; 2.3. SHAPE; 2.4. Inline probing; 2.5. Enzymatic cleavage
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2.6. Comparison of methods
Additional Edition:
Print version Computational Methods for Understanding Riboswitches
Language:
English
Subjects:
Biology
Keywords:
Riboswitch
;
Computerunterstütztes Verfahren
;
Aufsatzsammlung
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