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

1. Download all pdb files you intend to use as sources to some directory.
2. Prepare a list file that contains path/name.pdb for each source structure (see below)
3. 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