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Nucleic Acids Symposium Series 2006 50(1):67-68; doi:10.1093/nass/nrl033
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© 2006 Oxford University Press

High-throughput method for the prediction of low-resolution, three-dimensional RNA structures

Mariusz Popenda, Lukasz Bielecki and Ryszard W. Adamiak

Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland

Our aim is the high-throughput prediction of three-dimensional RNA structures at low resolution to answer questions posed by the RNA molecular biology. The strategy presented here is based on a computer program, called 3D-RNApredict, which implements and converts various structural data (RNA secondary structure, RNA motifs coordinates, experimental data) to create the input to the CYANA program (torsion-angle dynamics algorithm, TAD) which provides a fast engine for the 3D RNA structure calculation. The resultant RNA structure is refined using the X-PLOR program. The approach is amenable to automatization. Current predictions involve HIV-2 leader RNA domains and the sets of bacterial ncRNA.


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M. Popenda, M. Blazewicz, M. Szachniuk, and R. W. Adamiak
RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D386 - D391.
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