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).

• 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.