Theoretical Biochemistry Group

Institute for Theoretical Chemistry

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Basin hopping graph example BHGbuilder takes a list of local minima as input and constructs a basin hopping graph abstraction. Topology is abstracted from paths constructed by findpath procedure from ViennaRNA package. For every point on path, BHGbuilder searches for local minima by gradient path and stores connections between neighboring local minima basins. These connections are then being re-evaluated by flooding and printed to output. There is a multitude of options for interacting with BHG graph to obtain additional data out of graph, such as optimal refolding paths, or refolding rates.

For compiling BHGbuilder, you will need ViennaRNA package installed on your computer (tested with version 2.1.8). Then follow instructions in README.txt bundled with program. Run ./BHGbuilder -h to get help and available options.

In case you are using our software for your publications you may want to cite:

Basin Hopping Graph: A computational framework to characterize RNA folding landscapes
Marcel KucharĂ­k, Ivo L. Hofacker, Peter F. Stadler and Jing Qin
Bioinformatics 2014

Supplementary material to the publication above can be downloaded from here.


New release 2.0 is out!!! Added support for pseudoknots (actually a class called 1-structures) and reduction of the rate matrix for computation of kinetics. [11-05-2015]


The latest stable release is v2.0 and is provided as a source code zip file:
BHGbuilder v2.0 (zip, SourceCode) [79.7kB]

Old version v1.0:
BHGbuilder v1.0 (zip, SourceCode) [69.6kB]

You can also watch latest releases on GitHub: BHGbuilder GitHub! (Do not be misled by a former name of the program - DSUeval)

You can try the compiled program on test3.LM example. With command line: "BHGbuilder --graph-file=test3.eps --dot-energies < test3.LM" you should get the figure above with saddles.


In case of problems, found bugs, or need to chat, do not hesitate to contact us: -- programming -- ideas