Computational Methods for RNA Structure Validation and Improvement.

Jain, Swati

Richardson, David C

Richardson, Jane S

Woodson, SA

Allain, FHT

United States

2015-11-01T23:17:08Z

2015

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.

http://www.ncbi.nlm.nih.gov/pubmed/26068742

S0076-6879(15)00020-8

1557-7988

https://hdl.handle.net/10161/10807

eng

Elsevier

Methods Enzymol

10.1016/bs.mie.2015.01.007

Clash correction

ERRASER

MolProbity

PHENIX

RNA backbone conformers

RNA crystallography

Ribose pucker

wwPDB validation

Computational Biology

Crystallization

Crystallography, X-Ray

Data Interpretation, Statistical

Humans

Hydrogen Bonding

Models, Molecular

Nucleic Acid Conformation

RNA

RNA Folding

Ribostamycin

Software

Computational Methods for RNA Structure Validation and Improvement.

Journal article

Richardson, Jane S|0000-0002-3311-2944

http://www.ncbi.nlm.nih.gov/pubmed/26068742

181

212

Basic Science Departments

Biochemistry

Duke

Duke Cancer Institute

Institutes and Centers

School of Medicine

Published

558