Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide-nucleotide interactions from direct coupling analysis

Wang Jian, Kangkun Mao, Yunjie Zhao, Zeng Chen, Xiang Jianjin, Zhang Yi, Yi Xiao

Research output: Contribution to journalArticlepeer-review

85 Scopus citations

Abstract

Direct coupling analysis of nucleotide coevolution provides a novel approach to identify which nucleotides in an RNA molecule are likely in direct contact, and this information obtained from sequence only can be used to predict RNA 3D structures with much improved accuracy. Here we present an efficient method that incorporates this information into currentRNA3D structure predictionmethods, specifically 3dRNA. Our method makes much more accurate RNA 3D structure prediction than the original 3dRNA as well as other existing prediction methods that used the direct coupling analysis. In particular our method demonstrates a significant improvement in predicting multi-branch junction conformations, a major bottleneck for RNA 3D structure prediction. We also show that our method can be used to optimize the predictions by othermethods. These results indicate that optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide- nucleotide interactions from direct coupling analysis offers an efficient way for accurate RNA tertiary structure predictions.

Original languageEnglish (US)
Pages (from-to)6299-6309
Number of pages11
JournalNucleic acids research
Volume45
Issue number11
DOIs
StatePublished - Jun 1 2017

All Science Journal Classification (ASJC) codes

  • Genetics

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