Metadata

Authors:
Ingemar André (ingemar.andre@biochemistry.lu.se)
Sebastian Rämisch (raemisch@scripps.edu)

Corresponding PI: Ingemar André

Last edited 10/26/15.

Code

Application source code: rosetta/main/source/src/apps/public/struc_set_fragment_picker.cc

References

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,
Proteins (2015)
http://onlinelibrary.wiley.com/doi/10.1002/prot.24729/abstract;jsessionid=3B2AAEB6FBFDD42007B1A8DF5EABEA41.f04t03

Purpose

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.

Algorithm

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.

Notes

It does not use the scoring scheme used by the standard fragment picker
This will not work with JD2

How to run

Download all pdb files you intend to use as sources to some directory.
Prepare a list file that contains path/name.pdb for each source structure (see below)
Run struct_set_fragment_picker

Input

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
...

Options

Option	Explanation
-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.

Output

The output is a standard Rosetta fragment file to be used for structure prediction.

New things since last release

This is the first public release

Structure-Set-Fragment-Picker