SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.

Marcin Magnus,Michał J Boniecki,Janusz M Bujnicki,Wayne Dawson

doi:10.1093/nar/gkw279

Abstract

RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb.

Highlights

The ribonucleic acid (RNA) plays fundamental roles in biology, including the transmission of genetic information, regulation of gene expression and catalysis of biochemical reactions [1]
The SimRNAweb server is an automated and user-friendly implementation of SimRNA, a method for RNA 3D structure modeling developed in our laboratory [14] and used in practice in many cases, including participation in the RNA Puzzles experiment [21,22]
SimRNAweb has entered the new category of fully automated RNA 3D structure prediction of the RNA Puzzles competition

Summary

Introduction

The ribonucleic acid (RNA) plays fundamental roles in biology, including the transmission of genetic information, regulation of gene expression and catalysis of biochemical reactions [1]. A limited number of experimentally obtained RNA 3D structures are available in the Protein Data Bank [3], there are a multitude of RNA sequences [e.g. in the RNAcentral database [4]] for which no 3D structure exists. One must look at the 3D structure to gain a better appreciation for the mutual position of chemical groups that may be functionally relevant and interact with other molecules. This additional information about the 3D RNA structure is neither obvious nor intuitive from the sequence or secondary structure alone

Methods

Results

Conclusion