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Science 7 April 1989:
Vol. 244. no. 4900, pp. 48 - 52
DOI: 10.1126/science.2468181
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Articles

Science, Vol 244, Issue 4900, 48-52
Copyright © 1989 by American Association for the Advancement of Science

articles

On finding all suboptimal foldings of an RNA molecule

M Zuker

Division of Biological Sciences, National Research Council of Canada, Ottawa, Ontario.

An algorithm and a computer program have been prepared for determining RNA secondary structures within any prescribed increment of the computed global minimum free energy. The mathematical problem of determining how well defined a minimum energy folding is can now be solved. All predicted base pairs that can participate in suboptimal structures may be displayed and analyzed graphically. Representative suboptimal foldings are generated by selecting these base pairs one at a time and computing the best foldings that contain them. A distance criterion that ensures that no two structures are "too close" is used to avoid multiple generation of similar structures. Thermodynamic parameters, including free-energy increments for single-base stacking at the ends of helices and for terminal mismatched pairs in interior and hairpin loops, are incorporated into the underlying folding model of the above algorithm.


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