Nucleic Acids Res 9: 133-48 (1981)
Abstract
This paper presents a new computer method for folding an RNA molecule
that finds a conformation of minimum free energy using published values
of stacking and destabilizing energies. It is based on a dynamic
programming algorithm from applied mathematics, and is much more
efficient, faster, and can fold larger molecules than procedures which
have appeared up to now in the biological literature. Its power is
demonstrated in the folding of a 459 nucleotide immunoglobulin gamma 1
heavy chain messenger RNA fragment. We go beyond the basic method to
show how to incorporate additional information into the algorithm. This
includes data on chemical reactivity and enzyme susceptibility. We
illustrate this with the folding of two large fragments from the 16S
ribosomal RNA of Escherichia coli.
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