:: DESCRIPTION
MEPSA is a cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MEPSA: minimum energy pathway analysis for energy landscapes.
Marcos-Alcalde I, Setoain J, Mendieta-Moreno JI, Mendieta J, Gómez-Puertas P.
Bioinformatics. 2015 Jul 31. pii: btv453.
:: DESCRIPTION
Regliss proposes to study the energy landscape of a given RNA sequence by considering all locally optimal structures.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
J Comput Biol. 2012 Oct;19(10):1120-33. doi: 10.1089/cmb.2010.0178.
RNA locally optimal secondary structures.
Saffarian A, Giraud M, de Monte A, Touzet H.
:: DESCRIPTION
FFTbor computes Boltzmann probability for RNA structural neighbors using the fast Fourier transform.
Given an RNA sequence having metastable secondary structures A,B, the program FFTbor2D computes the ensemble free energy E(x,y)=-RT log Z(x,y), taken over all secondary structures having base pair distance x from A,and base pair distance y from B.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PLoS One. 2012;7(12):e50506. doi: 10.1371/journal.pone.0050506. Epub 2012 Dec 19.
Using the fast fourier transform to accelerate the computational search for RNA conformational switches.
Senter E1, Sheikh S, Dotu I, Ponty Y, Clote P.
J Math Biol. 2015 Jan;70(1-2):173-96. doi: 10.1007/s00285-014-0760-4. Epub 2014 Feb 12.
RNA folding pathways and kinetics using 2D energy landscapes.
Senter E1, Dotu I, Clote P.
