Corresponding PI: Ingemar André
Last edited 10/26/15.
This simple fragment set generator was first used in:
Sebastian Rämisch, Robert Lizatovic and Ingemar André,
Exploring alternate states and oligomerization preferences of coiled-coils by de novo structure modeling,
Generate fragment sets for Rosetta protein structure modeling using a predefined set of protein structures as fragment source. The fragments are randomly picked from a set of structures, irrespective of sequence and secondary structure. The original intention was to predict coiled-coil structures using exclusively fragments taken from coiled-coil structures.
First, all possible fragments from a given set of PDB files are generated. Then, for each position of the target sequence, a set of fragments (default=200) is randomly picked. Secondary structure and sequence are not considered at any point.
The only input file is a list of the pdb names to be used. E.g.:
input/struct_files/1e5t.pdb input/struct_files/3tg7.pdb input/struct_files/2guv.pdb ...
|-in::file::l||list of structures|
|-frags:n_frags||number of fragments per position (optional; default = 200)|
|-struc_set_fragment_picker::frag_length||Fragment length. Usually 3 or 9.|
|-struc_set_fragment_picker::sequence_length||Length of target sequence.|
|-struc_set_fragment_picker::frag_name||Name of the output fragment file. Usually 5 characters.|
The output is a standard Rosetta fragment file to be used for structure prediction.
This is the first public release