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Updated: Aug 12, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Nucleic Acid Structure Prediction Including Pseudoknots Through Direct Enumeration of States: A User's Guide to the
Ofer Kimchi1,2, Michael P Brenner3, Lucy J Colwell4
1School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA. okimchi@princeton.edu.
Abstract:
Here we detail the LandscapeFold secondary structure prediction algorithm and how it is used. The algorithm was previously described and tested in (Kimchi O et al., Biophys J 117(3):520-532, 2019), though it was not named there. The algorithm directly enumerates all possible secondary structures into which up to two RNA or single-stranded DNA sequences can fold. It uses a polymer physics model to estimate the configurational entropy of structures including complex pseudoknots. We detail each of these steps and ways in which the user can adjust the algorithm as desired. The code is available on the GitHub repository https://github.com/ofer-kimchi/LandscapeFold .
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