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Computational Methods for RNA Structure Validation and Improvement.

dc.contributor.author Jain, S
dc.contributor.author Richardson, DC
dc.contributor.author Richardson, JS
dc.coverage.spatial United States
dc.date.accessioned 2015-11-01T23:17:08Z
dc.date.issued 2015
dc.identifier http://www.ncbi.nlm.nih.gov/pubmed/26068742
dc.identifier S0076-6879(15)00020-8
dc.identifier.uri http://hdl.handle.net/10161/10807
dc.description.abstract With increasing recognition of the roles RNA molecules and RNA/protein complexes play in an unexpected variety of biological processes, understanding of RNA structure-function relationships is of high current importance. To make clean biological interpretations from three-dimensional structures, it is imperative to have high-quality, accurate RNA crystal structures available, and the community has thoroughly embraced that goal. However, due to the many degrees of freedom inherent in RNA structure (especially for the backbone), it is a significant challenge to succeed in building accurate experimental models for RNA structures. This chapter describes the tools and techniques our research group and our collaborators have developed over the years to help RNA structural biologists both evaluate and achieve better accuracy. Expert analysis of large, high-resolution, quality-conscious RNA datasets provides the fundamental information that enables automated methods for robust and efficient error diagnosis in validating RNA structures at all resolutions. The even more crucial goal of correcting the diagnosed outliers has steadily developed toward highly effective, computationally based techniques. Automation enables solving complex issues in large RNA structures, but cannot circumvent the need for thoughtful examination of local details, and so we also provide some guidance for interpreting and acting on the results of current structure validation for RNA.
dc.language eng
dc.relation.ispartof Methods Enzymol
dc.relation.isversionof 10.1016/bs.mie.2015.01.007
dc.subject Clash correction
dc.subject ERRASER
dc.subject MolProbity
dc.subject PHENIX
dc.subject RNA backbone conformers
dc.subject RNA crystallography
dc.subject Ribose pucker
dc.subject wwPDB validation
dc.subject Computational Biology
dc.subject Crystallization
dc.subject Crystallography, X-Ray
dc.subject Data Interpretation, Statistical
dc.subject Humans
dc.subject Hydrogen Bonding
dc.subject Models, Molecular
dc.subject Nucleic Acid Conformation
dc.subject RNA
dc.subject RNA Folding
dc.subject Ribostamycin
dc.subject Software
dc.title Computational Methods for RNA Structure Validation and Improvement.
dc.type Journal article
pubs.author-url http://www.ncbi.nlm.nih.gov/pubmed/26068742
pubs.begin-page 181
pubs.end-page 212
pubs.organisational-group Basic Science Departments
pubs.organisational-group Biochemistry
pubs.organisational-group Duke
pubs.organisational-group Duke Cancer Institute
pubs.organisational-group Institutes and Centers
pubs.organisational-group School of Medicine
pubs.publication-status Published
pubs.volume 558
dc.identifier.eissn 1557-7988


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