RNA tertiary structure prediction with ModeRNA

M. Rother, K. Rother, T. Puton, J. M. Bujnicki
2011 Briefings in Bioinformatics  
Noncoding RNAs perform important roles in the cell. As their function is tightly connected with structure, and as experimental methods are time-consuming and expensive, the field of RNA structure prediction is developing rapidly. Here, we present a detailed study on using the ModeRNA software. The tool uses the comparative modeling approach and can be applied when a structural template is available and an alignment of reasonable quality can be performed. We guide the reader through the entire
more » ... ocess of modeling Escherichia coli tRNA Thr in a conformation corresponding to the complex with an aminoacyl-tRNA synthetase (aaRS). We describe the choice of a template structure, preparation of input files, and explore three possible modeling strategies. In the end, we evaluate the resulting models using six alternative benchmarks. The ModeRNA software can be freely downloaded from Magdalena Rother is the main author of ModeRNA. She prepared the modeling case study presented in this article. Kristian Rother is a software developer and bioinformatician working on RNA 3D modeling. He is a co-developer of the ModeRNA software. Tomasz Puton is a structural bioinformatician working on procedures for RNA 2D structure prediction. He has also experience with RNA 3D modeling and is a co-developer of the ModeRNA software. Janusz M. Bujnicki is a head of the group, an initiator and a supervisor of the ModeRNA project.
doi:10.1093/bib/bbr050 pmid:21896613 fatcat:ajfiewysjrfwzcrr6qtqnfz4eu