RNA 3D Structure Analysis and Prediction [1 ed.] 3642257399, 9783642257391
With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly
194 77 55KB
English Pages 402 [411] Year 2012
Table of contents :
Front Matter....Pages i-x
Introduction....Pages 1-3
Modeling RNA Molecules....Pages 5-17
Methods for Predicting RNA Secondary Structure....Pages 19-41
Why Can’t We Predict RNA Structure At Atomic Resolution?....Pages 43-65
Template-Based and Template-Free Modeling of RNA 3D Structure: Inspirations from Protein Structure Modeling....Pages 67-90
The RNA Folding Problems: Different Levels of sRNA Structure Prediction....Pages 91-117
Computational Prediction and Modeling Aid in the Discovery of a Conformational Switch Controlling Replication and Translation in a Plus-Strand RNA Virus....Pages 119-142
Methods for Building and Refining 3D Models of RNA....Pages 143-166
Multiscale Modeling of RNA Structure and Dynamics....Pages 167-184
Statistical Mechanical Modeling of RNA Folding: From Free Energy Landscape to Tertiary Structural Prediction....Pages 185-212
Simulating Dynamics in RNA–Protein Complexes....Pages 213-238
Quantum Chemical Studies of Recurrent Interactions in RNA 3D Motifs....Pages 239-279
Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking....Pages 281-298
Ions in Molecular Dynamics Simulations of RNA Systems....Pages 299-318
Modeling RNA Folding Pathways and Intermediates Using Time-Resolved Hydroxyl Radical Footprinting Data....Pages 319-334
A Top-Down Approach to Determining Global RNA Structures in Solution Using NMR and Small-Angle X-ray Scattering Measurements....Pages 335-359
RNA Structure Determination by Structural Probing and Mass Spectrometry: MS3D....Pages 361-389
Back Matter....Pages 391-400
Front Matter....Pages i-x
Introduction....Pages 1-3
Modeling RNA Molecules....Pages 5-17
Methods for Predicting RNA Secondary Structure....Pages 19-41
Why Can’t We Predict RNA Structure At Atomic Resolution?....Pages 43-65
Template-Based and Template-Free Modeling of RNA 3D Structure: Inspirations from Protein Structure Modeling....Pages 67-90
The RNA Folding Problems: Different Levels of sRNA Structure Prediction....Pages 91-117
Computational Prediction and Modeling Aid in the Discovery of a Conformational Switch Controlling Replication and Translation in a Plus-Strand RNA Virus....Pages 119-142
Methods for Building and Refining 3D Models of RNA....Pages 143-166
Multiscale Modeling of RNA Structure and Dynamics....Pages 167-184
Statistical Mechanical Modeling of RNA Folding: From Free Energy Landscape to Tertiary Structural Prediction....Pages 185-212
Simulating Dynamics in RNA–Protein Complexes....Pages 213-238
Quantum Chemical Studies of Recurrent Interactions in RNA 3D Motifs....Pages 239-279
Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking....Pages 281-298
Ions in Molecular Dynamics Simulations of RNA Systems....Pages 299-318
Modeling RNA Folding Pathways and Intermediates Using Time-Resolved Hydroxyl Radical Footprinting Data....Pages 319-334
A Top-Down Approach to Determining Global RNA Structures in Solution Using NMR and Small-Angle X-ray Scattering Measurements....Pages 335-359
RNA Structure Determination by Structural Probing and Mass Spectrometry: MS3D....Pages 361-389
Back Matter....Pages 391-400
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- Author / Uploaded
- Michael Levitt (auth.)
- Neocles Leontis
- Eric Westhof (eds.)
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