The online demo of CCFold is available here.
If you use this program, please cite Guzenko, D., Strelkov, S. V. (2017). CCFold: rapid and accurate prediction of coiled-coil structures and application to modelling intermediate filaments. Bioinformatics.
Coiled coils folding and intermediate filament models. Please see the 'Validation' folder if you want to reproduce the benchmarking results in our paper. For an example of how to generate the fragment libraries, look into the scripts in the 'Fragments' folder.
Usage: CCFold.py [-h] [-n 2|3] [-s] [-t one|termini|all] [-sp 100] [-bp 350] [-spp 50]
sequence [output_dir]
Positional arguments:
sequence Fasta file with the target sequence (hmodimer),
or a pair of aligned sequences (heterodimer).
output_dir Directory to output the model files.
Optional arguments:
-h, --help Show this help message and exit
-n 2|3 Number of helices in a coiled coil. 2 (default) or 3 are
supported at the moment.
-s Straighten the model. Prefer symmetric output at some
cost to smoothness. Number of fragments tried for each
segment is defined by the -spp parameter.
-t one|termini|all Produce single model (default), vary termini or vary
fragments in all windows. Number of fragments to vary is
defined by the -spp parameter.
-sp 100 Number of fragments to consider for initial
segmentation.
-bp 350 Number of fragments to pick for mutual alignment.
-spp 50 Number of fragments to use in shortest path outputs.