RNA tertiary structure prediction with ModeRNA
| Autor: | Magdalena Rother, Janusz M. Bujnicki, Tomasz Puton, Kristian Rother |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2011 |
| Předmět: |
Models
Molecular Computer science Protein Conformation Molecular Sequence Data 010402 general chemistry computer.software_genre 01 natural sciences Field (computer science) World Wide Web Amino Acyl-tRNA Synthetases 03 medical and health sciences Software RNA Transfer Molecular Biology 030304 developmental biology Structure (mathematical logic) 0303 health sciences Base Sequence business.industry Nucleic acid tertiary structure Programming language Process (computing) Function (mathematics) Mac OS 0104 chemical sciences Rna structure prediction Nucleic Acid Conformation RNA business computer Sequence Alignment Information Systems |
| Zdroj: | Briefings in Bioinformatics |
| ISSN: | 1467-5463 |
| DOI: | 10.1093/bib/bbr050 |
| Popis: | 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 process 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 http://iimcb.genesilico.pl/moderna/ under the conditions of the General Public License. It runs under LINUX, Windows and Mac OS. It is also available as a server at http://iimcb.genesilico.pl/modernaserver/. The models and the script to reproduce the study from this article are available at http://www.genesilico.pl/moderna/examples/. |
| Databáze: | OpenAIRE |
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