fragments.README

FOR ACADEMIC USE ONLY.

WEBSERVER FOR FRAGMENTS:
http://robetta.bakerlab.org/fragmentsubmit.jsp

TO MAKE FRAGMENTS LOCALLY WITH make_fragments.pl:

The Rosetta software package is available at https://www.rosettacommons.org


PLATFORM REQUIREMENT: Linux


SETUP:

  1. BUILD ROSETTA FRAGMENT PICKER

     $> cd ../../main/source

     #  Modify -j 20 for the number of CPUs to use for compiling.

     # External boost_thread libraries are required for multi-threaded fragment picking
     #   The Rosetta boost version is `ls -d external/boost_*`

     $> scons mode=release extras=boost_thread bin/fragment_picker.boost_thread.linuxgccrelease -j 20

     # or do a standard build

     $> scons mode=release bin/fragment_picker.linuxgccrelease -j 20

  2. OPTIONAL

     For a custom setup, modify the configuration at the top of make_fragments.pl


USAGE:

  1. Obtain a fasta file for the desired sequence. First
     line can be a comment starting with the '>' character.

  2. Run make_fragments.pl.
     Invoke without arguments for initial installation and usage options.
     External dependencies are downloaded and installed automatically the first time you run make_fragments.pl.
     The initial installation takes a long time because the NCBI non-redundant (nr) sequence database is very
     large so please be patient.

     Likely the only argument you need to provide is the fasta file.

     $> make_fragments.pl -verbose 2ptl_.fasta

     If you want to exclude homologous seqeunces from the fragment search,
     add the -nohoms argument.

     $> make_fragments.pl -verbose -nohoms 2ptl_.fasta


REFERENCES:

Rosetta fragment picker reference:

 Gront, D., Kulp, D.W., Vernon, R.M., Strauss, C.E.M. & Baker, D. Generalized fragment picking in Rosetta:
 design, protocols and applications. PLoS ONE 6, e23294 (2011).


Please use the following references for external dependencies:

- NCBI Blast (http://www.ncbi.nlm.nih.gov/blast/blast_references.shtml)

 Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J (1997) "Gapped
 BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res. 25:3389-3402

- SPARKS-X (http://sparks-lab.org/yueyang/server/SPARKS-X/)

 Yuedong Yang, Eshel Faraggi, Huiying Zhao, Yaoqi Zhou. Improving protein fold recognition and template-based
 modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of
 the query and corresponding native properties of templates. Bioinformatics 27:2076-82(2011)

- Psipred (http://bioinf.cs.ucl.ac.uk/psipred/)

 Jones DT. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol.
 Biol. 292: 195-202.