Compannotate: A Comparative Approach To Annotate Base-Pairing Interactions In Rna 3D Structures

Abstract

The analysis of RNA tertiary structure is hindered by the fact that not too many structural data are available and a significant amount of them are in low resolution. Due to the atomic coordinate errors posed by the limitations of low-resolution RNA three-dimensional structures, it becomes a critical challenge to extract key geometric characteristics of RNA, particularly, the interaction of bases. To address this issue, we have devised a comparative method, named CompAnnotate, that utilizes more precise structural information of high-resolution homologs to annotate the base-pairing interactions in the low-resolution structures, by aligning and making comparative geometric assessments. The benchmarking results show that our method can improve the annotations of the existing methods significantly. We have achieved different levels of improvements for various methods and datasets, including an example of significant sensitivity and precision enhancement from 28 to 57% and from 53 to 82%, respectively.

Publication Date

8-21-2017

Publication Title

Nucleic acids research

Volume

45

Issue

14

Number of Pages

e136-

Document Type

Article

Personal Identifier

scopus

DOI Link

https://doi.org/10.1093/nar/gkx538

Socpus ID

85031848967 (Scopus)

Source API URL

https://api.elsevier.com/content/abstract/scopus_id/85031848967

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