3dRNA v2.0: An Updated Web Server for RNA 3D Structure Prediction.

Jun Wang,Yanzhao Huang,Yi Xiao,Jian Wang

doi:10.3390/ijms20174116

Jun Wang, Yanzhao Huang + Show 2 more

Open Access

https://doi.org/10.3390/ijms20174116

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Abstract

3D structures of RNAs are the basis for understanding their biological functions. However, experimentally solved RNA 3D structures are very limited in comparison with known RNA sequences up to now. Therefore, many computational methods have been proposed to solve this problem, including our 3dRNA. In recent years, 3dRNA has been greatly improved by adding several important features, including structure sampling, structure ranking and structure optimization under residue-residue restraints. Particularly, the optimization procedure with restraints enables 3dRNA to treat pseudoknots in a new way. These new features of 3dRNA can greatly promote its performance and have been integrated into the 3dRNA v2.0 web server. Here we introduce these new features in the 3dRNA v2.0 web server for the users.

Highlights

Noncoding RNAs can catalyze and regulate many biochemical reactions in organisms [1]
This optimization method can greatly increase the accuracy of the predicted structures using 3dRNA, as well as other RNA 3D structure prediction methods [24]
We have implemented an algorithm of direct coupling analysis (DCA) [25] to find the most likely contacted nucleotide pairs that can be used as the restraints in the optimization procedure

Summary

Introduction

Noncoding RNAs can catalyze and regulate many biochemical reactions in organisms [1]. The number of solved RNA 3D structures is still quite small compared with the large amount of non-coding RNA sequences and this becomes an obstacle to explore their functions. Many computational methods have been proposed for predicting the 3D structure of non-coding RNA, e.g., FARNA [2]/FARFAR [3], MC-Sym [4], NAST [5], iFoldRNA [6,7], ASSEMBLE [8], Vfold [9,10], RNAComposer [11,12], 3dRNA [13,14,15] and F-RAG [16]. 3dRNA is an automated method of building RNA 3D structures from sequences and secondary structures by using the smallest secondary elements (SSEs) [14]. The 3dRNA v2.0 web server can be accessed at http://biophy.hust.edu.cn/3dRNA

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Conclusion