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Bioinformatics Advance Access originally published online on February 24, 2005
Bioinformatics 2005 21(10):2356-2361; doi:10.1093/bioinformatics/bti351
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

RNA tertiary structure determination: NOE pathways construction by tabu search

Jacek Blazewicz 1,2, Marta Szachniuk 1,* and Adam Wojtowicz 2

1Istitute of Bioorganic Chemistry, Polish Academy of Sciences 61-704 Poznan, Poland
2Institute of Computing Science, Poznan University of Technology 60-965 Poznan, Poland

*To whom correspondence should be addressed.

Motivation: Liquid state nuclear magnetic resonance (NMR) spectroscopy has now been well established as a method for RNA tertiary structure determination. Most of the steps involved in the determination of RNA molecules are performed using computer programs. They however, do not apply to resonance assignment being the starting point of the whole procedure. We propose a tabu search algorithm as a tool for automating this step. Nuclear overhause effect (NOE) pathway, which determines the assignment, is constructed during an analysis of possible connections between resonances within aromatic/anomeric region of two-dimensional NOESY spectrum resulting from appropriate NMR experiment.

Results: Computational tests demonstrate the superior performance of the tabu search algorithm as compared with the exact enumerative approach and genetic procedure applied to the experimental and simulated spectral data for RNA molecules.

Availability: The software package can be obtained upon request from Marta Szachniuk.

Contact: mszachniuk{at}cs.put.poznan.pl


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