Tools for modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure
This page provides the source code for programs described in
R. Forties and R. Bundschuh, Modeling the interplay of single-stranded
binding proteins and nucleic acid secondary structure.
Bioinformatics 26, 61-7 (2010).
Our modified package is based on version 1.4 of the Vienna package. The original Vienna RNA secondary structure package may be found at http://www.tbi.univie.ac.at/RNA/.
The source code to our modified Vienna package.
To compile the package, you will need the GNU Scientific library, availabe from http://www.gnu.org/software/gsl/. You will also of course need a C compiler. You should then be able to compile the package by just typing "make" in the top level directory.
The program used to calculate the FRET distributions and other observables described in our paper is RNAdist. You will need to run this program from a directory containing the files "NC_Energies.dat" and "m_to_FRET_dist.txt". These files are located in the /bin directory of the package. "NC_Energies.dat" contains protein binding parameters, allowing these to be edited without recompiling the package. "m_to_FRET_dist.txt" contains the FRET distribution as a function of number of exterior bases "m" under the conditions described in our paper.
10/12/2009 Robert Forties