A new kinetic metric from spectral analysis of transition rates is applied to RNA energy landscapes, showing that ultrametricity depends on nucleotide order for fixed composition.
Zuker,On finding all suboptimal foldings of an RNA molecule, Science244, 48–52 (1989)
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Numerical examination of ultrametricity in Nussinov-model RNA energy minima shows wide variation across 18 RNAs and strong sensitivity to nucleotide sequence permutation.
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Kinetic metric for basins of attraction of RNA secondary structures and analysis of the ultrametricity of the energy landscape
A new kinetic metric from spectral analysis of transition rates is applied to RNA energy landscapes, showing that ultrametricity depends on nucleotide order for fixed composition.
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Ultrametricity of Energy Minimum Configurations of RNA Secondary Structures in the Nussinov Model
Numerical examination of ultrametricity in Nussinov-model RNA energy minima shows wide variation across 18 RNAs and strong sensitivity to nucleotide sequence permutation.