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Energy parameters and novel algorithms for an extended nearest neighbor energy model of RNA
Complete RNA inverse folding
RNAiFold
Using RNA inverse folding to identify IRES-like structural subdomains
Asymptotic structural properties of quasi-random saturated structures of RNA
Integrating chemical footprinting data into RNA secondary structure prediction
Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches
Maximum expected accuracy structural neighbors of an RNA secondary structure
Computing the partition function for kinetically trapped RNA secondary structures
Thermodynamics of RNA structures by Wang-Landau sampling
Computing folding pathways between RNA secondary structures