Assigning NMR spectra of irregular RNAs by heuristic algorithms

Abstract

Abstract.Computer-aided analysis and preprocessing of spectral data is a prerequisite for any study of molecular structures by Nuclear Magnetic Resonance (NMR) spectroscopy. The data processing stage usually involves a considerable dedication of time and expert knowledge to cope with peak picking, resonance signal assignment and calculation of structure parameters. A significant part of the latter step is performed in an automated way. However, in peak picking and resonance assignment a multistage manual assistance is still essential. The work presented here is focused on the theoretical modeling and analyzing the assignment problem by applying heuristic approaches to the NMR spectra recorded for RNA structures containing irregular regions.

RNApolis: Computational Platform for RNA Structure Analysis

“…The developing branch of structural biology, whose aim was to learn about the structure of molecules and to discover the structure-function relationship, only occasionally touched upon the subject of RNA. This was due not only to the low interest in this molecule but also to the difficulty of studying and determining the RNA structure with experimental methods [1,21,41,52,53].…”

“…The 3D structure of RNA can be assessed in the experimental or computational way. The first approach utilizes experiments like X-ray crystallography or NMR spectroscopy and applies computational tools that support processing and analysis of experimental data [1,52]. In the second one, the structure is predicted from the sequence by in silico methods [4,19,34].…”