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Bioinformatics Advance Access published online on February 24, 2005
Bioinformatics, 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@oupjournals.org
Received January 23, 2005
Revised February 20, 2005
Accepted February 22, 2005

Article

RNA tertiary structure determination: NOE pathways construction by tabu search

Jacek Blazewicz 1, Marta Szachniuk 2*, and Adam Wojtowicz 3

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

* To whom correspondence should be addressed.
Marta Szachniuk, E-mail: mszachniuk{at}cs.put.poznan.pl


  Abstract

Motivation: Liquid state Nuclear Magnetic Resonance (NMR) spectroscopy has been now well established as a method for RNA tertiary structure determination. Most of the steps of the determination process for RNA molecules are performed with the use of computer programs which, however, do not apply to a resonance assignment being the starting point of the whole procedure. We propose a tabu search algorithm being a tool for an automatization of this step. NOE pathway, which determines the assignment, is constructed during an analysis of possible connections between resonances within aromatic/anomeric region of 2D-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 by request to Marta Szachniuk.


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