RNA helix indexes as a tool for RNA folding space analysis

• Applicant: Professor Dr. Björn Voß
• Subject Area: Bioinformatics and Theoretical Biology
• Term: from 2009 to 2013
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 164256295

The biological function of an RNA is mainly given by its spatial arrangement. This three dimensional structure is primarily assembled through the formation of base pairs by hydrogen-bonding, the so called secondary structure. The latter can be predicted using dynamic programming algorithms, which rely on thermodynamic parameters for the base interactions. Often it is not sufficient to take only the optimal structure into account. For example, problems such as conformational switching or traps within the folding path (local minima) can only be addressed, if all or a reasonably large number of structures are analyzed. This means that the complete or a part of the folding space has to be considered. Here I propose a project which enables folding space analysis based on an abstraction mechanism, which significantly reduces the size while maintaining the characteristics of the folding space. This abstraction is based on describing structures as lists of helix indexes and keeps only those which are composed of different helices. This technique is known as shape abstraction and has proven its power for RNA structure analysis. The tools to be developed will address problems in folding space analysis, such as prediction of energy barriers and local minima. Due to the abstraction the tools will provide fast and efficient algorithms covering the before mentioned aspects and will enable in-depth analyses such as simulating folding kinetics for reasonably long RNA molecules.

• DFG Programme: Research Grants