Author: Jianqing Xu (xubest@gmail.com), Daisuke Kuroda (dkuroda1981@gmail.com), Oana Lungu (olungu@utexas.edu), Jeffrey Gray (jgray@jhu.edu)
Corresponding PI Jeffrey Gray (jgray@jhu.edu).
Last edited 9/28/2014 by Jared Adolf-Bryfogle.
We recommend the following articles for further studies of RosettaDock methodology and applications:
This is a python script for pre-processing for the antibody protocol (developer only repository): https://svn.rosettacommons.org/source/trunk/antibody/scripts.v2/
The script consists of 3 main steps:
Inputs:
Also, you can specify templates by using options –L1=<PDB ID 1>, –L2=<PDB ID 2> etc. See all options below.
Outputs:
Minimal usage:
./antibody.py --light-chain <input_l.fasta> --heavy-chain <input_h.fasta> --blast=<blast> --blast-database=<blast_database>The final outputs are below. In this case, you have to graft templates by yourself. FR.pdb (FR template and CDR dummy coordinates) L1.pdb, L2.pdb, L3.pdb, H1.pdb, H2.pdb, H3.pdb (template of each CDR)
Complete usage for grafting:
./antibody.py --light-chain <input_l.fasta> --heavy-chain <input_h.fasta> --profit=<ProFit> --blast=<blast> --blast-database=<blast_database> --antibody-database=<antibody_database> --rosetta-bin=<rosetta/rosetta_sourse/bin> --rosetta-database=<rosetta_database> The final outputs are below.
Usage: antibody.py [OPTIONS] [TESTS]
Script for preparing detecting antibodys and preparing info for Rosetta
protocol.
Options:
-h, --help show this help message and exit
-L LIGHT_CHAIN, --light-chain=LIGHT_CHAIN
Specify file with the light chain - pure IUPAC ASCII
letter sequence, no FASTA headers.
-H HEAVY_CHAIN, --heavy-chain=HEAVY_CHAIN
Specify file with the heavy chain - pure IUPAC ASCII
letter sequence, no FASTA headers.
--prefix=PREFIX Prefix for output files (directory name). Default is
grafting/.
--blast=BLAST Specify path+name for 'blastall' executable. Default
is blastp [blast+].
--superimpose-profit=SUPERIMPOSE_PROFIT
(default). Add full path as argument if necessary.
--superimpose-PyRosetta, --superimpose-pyrosetta
Use PyRosetta to superimpose interface (boolean)
--blast-database=BLAST_DATABASE
Specify path of blast database dir.
--antibody-database=ANTIBODY_DATABASE
Specify path of antibody database dir. Default:
script_dir/antibody_database.
--rosetta-database=ROSETTA_DATABASE
Specify path of rosetta database dir.
-x, --exclude-homologs
Exclude homologs with default cutoffs
--homolog_exclusion=HOMOLOG_EXCLUSION
Specify the cut-off for homolog exclusion during CDR
or FR template selections.
--homolog_exclusion_cdr=HOMOLOG_EXCLUSION_CDR
Specify the cut-off for homolog exclusion during CDR
template selections.
--homolog_exclusion_fr=HOMOLOG_EXCLUSION_FR
Specify the cut-off for homolog exclusion during FR
template selections.
--rosetta-bin=ROSETTA_BIN
Specify path to 'rosetta/source/bin' directory,
expected to harbor 'antibody_graft', 'idealize' and
'relax' executables. Default is
'$ROSETTA/main/source/bin, then <script location>/bin'
(place symlink there). If a particular executable is
not found and that is non-critical, corresponding
steps will be skipped.
--rosetta-platform=ROSETTA_PLATFORM
Specify full extra+compiler+build type for rosetta
binaries found in --rosetta-bin. For example use
static.linuxgccrelease for static build on Linux.
Default are dynamic GCC release builds of the OS
executing the script.
--idealize Use idealize protocol on final model.
--constant-seed Use constant-seed flag in Rosetta grafting run (for
debugging).
--idealizeoff, --noidealize
Do not use idealize protocol on final model. (default)
--relax Use relax protocol on final model. (default)
--relaxoff, --norelax
Do not use relax protocol on final model.
--skip-kink-constraints
Skip generation of kink constraints file (require
PyRosetta). Default is True.
--timeout=TIMEOUT Maximum runtime for rosetta relax run (use 0 for
unlimit), default is 900 - 15min limit
-q, --quick Specify fast run (structure will have clashes).
Prevents stem optimization and turns off relax,
idealize.
--FRL=FRL Specify path or PDB code for FRL template. If
specified this will overwrite blast selection.
--FRH=FRH Specify path or PDB code for FRH template. If
specified this will overwrite blast selection.
--light=LIGHT Specify path or PDB code for light template. If
specified this will overwrite blast selection.
--heavy=HEAVY Specify path or PDB code for heavy template. If
specified this will overwrite blast selection.
--L1=L1 Specify path or PDB code for L1 template. If specified
this will overwrite blast selection.
--L2=L2 Specify path or PDB code for L2 template. If specified
this will overwrite blast selection.
--L3=L3 Specify path or PDB code for L3 template. If specified
this will overwrite blast selection.
--H1=H1 Specify path or PDB code for H1 template. If specified
this will overwrite blast selection.
--H2=H2 Specify path or PDB code for H2 template. If specified
this will overwrite blast selection.
--H3=H3 Specify path or PDB code for H3 template. If specified
this will overwrite blast selection.
--light_heavy=LIGHT_HEAVY
Specify path or PDB code for light_heavy template. If
specified this will overwrite blast selection.
--self-test Perform self test by using data in test/ dir and exit.
--self-test-dir=SELF_TEST_DIR
Specify path for self test dir [default:self-test/].
-v, --verbose Generate verbose output.
--filter-by-outlier=FILTER_BY_OUTLIER
Boolean option [0/1] that control filetering results
with filter_by_outlier function.
--filter-by-sequence-length=FILTER_BY_SEQUENCE_LENGTH
Boolean option [0/1] that control filetering results
with filter_by_sequence_length function.
--filter-by-alignment-length=FILTER_BY_ALIGNMENT_LENGTH
Boolean option [0/1] that control filetering results
with filter_by_alignment_length function.
--filter-by-template-resolution=FILTER_BY_TEMPLATE_RESOLUTION
Boolean option [0/1] that control filetering results
with filter_by_template_resolution function.
--filter-by-sequence-homolog=FILTER_BY_SEQUENCE_HOMOLOG
Boolean option [0/1] that control filetering results
with filter_by_sequence_homolog function.
--filter-by-template-bfactor=FILTER_BY_TEMPLATE_BFACTOR
Boolean option [0/1] that control filetering results
with filter_by_template_bfactor function.
This is the first public release in Rosetta3
Antibody Applications: Homepage for antibody applications
Antibody Design Strategy Analysis: A PyRosetta-based tool to analyze and/or compare antibody design strategies.
CDR Cluster Identification: An application that matches each CDR of an antibody to North/Dunbrack CDR clusters based on the lowest dihedral distance to each cluster center.