RosettaAntibody3: a). The PreProcessing Python Script
Metadata
Author: Jianqing Xu (xubest@gmail.com), Daisuke Kuroda (dkuroda1981@gmail.com), Oana Lungu (olungu@utexas.edu), Jeffrey Gray (jgray@jhu.edu)
Last edited 4/25/2013. Corresponding PI Jeffrey Gray (jgray@jhu.edu).
References
We recommend the following articles for further studies of RosettaDock methodology and applications:
- J. Xu, D. Kuroda & J. J. Gray, “RosettaAntibody3: Object-Oriented Designed Protocol and Improved Antibody Homology Modeling.” (2013) in preparation
- A. Sivasubramanian,* A. Sircar,* S. Chaudhury & J. J. Gray, "Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking," Proteins 74(2), 497-514 (2009)
Application purpose
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:
- templates selection by BLAST,
- grafting by Rosetta executable
- optimize the grafted model by Rosetta protocols. In the step 3, FastRelax w/ all-atom constraint is used. this step make template Phi/Psi values better.
Inputs:
- Sequence of the light chain Fv in FASTA format
- Sequence of the heavy chain Fv in FASTA format
Also, you can specify templates by using options –L1=<PDB ID 1>, –L2=<PDB ID 2> etc. See all options below.
Outputs:
- Sequence-grafted and refined Fv pdb: grafted.pdb, grafted.relaxed.pdb
- Constraints file for optional use in Step 3: cter_constraint
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.
- grafted.pdb (grafted model)
- grafted.relaxed.pdb (grafted relaxed model)
- cter_constraint (kink/extend constraint file)
Options
Options of the script:
-h, --help show this help message and exit
--light-chain=LIGHT_CHAIN
Specify the light chain.
--heavy-chain=HEAVY_CHAIN
Specify the heavy chain.
--prefix=PREFIX Prefix for output files. Should be dir name. Default
is ./ string.
--blast=BLAST Specify path+name for 'blastall' executable. Default
is blastp [blast+].
--profit=PROFIT Specify path+name for 'ProFIt' executable. Default is
profit.
--blast-database=BLAST_DATABASE
Specify path of blast database dir.
--antibody-database=ANTIBODY_DATABASE
Specify path of antibody database dir.
--rosetta-database=ROSETTA_DATABASE
Specify path of rosetta database dir.
--rosetta-bin=ROSETTA_BIN
Specify path to 'rosetta_source/bin' dir where
antibody_assemble_CDRs', idealize and relax executable
expected to be found. Default is '<script
location>/bin' (plasce symlink there) and if not found
corresponding steps will be skipped.
--rosetta-platform=ROSETTA_PLATFORM
Specify full extra+compier+build type for rosetta
biniaries found in --rosetta-bin. For example use
static.linuxgccrelease for static build on Linux.
Default is dynamic release build of current OS
--idealize=IDEALIZE Specify if idealize protocol should be running on
final model [0/1]. (default: 0, which mean do not run
idealize protocol)
--relax=RELAX Specify if relax protocol should be running on final
model [0/1]. (default: 1, which mean run relax
protocol)
--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-sequence-length=FILTER_BY_SEQUENCE_LENGTH
Boolen option [0/1] that control filetering results
with filter_by_sequence_length function.
--filter-by-template-bfactor=FILTER_BY_TEMPLATE_BFACTOR
Boolen option [0/1] that control filetering results
with filter_by_template_bfactor function.
--filter-by-outlier=FILTER_BY_OUTLIER
Boolen option [0/1] that control filetering results
with filter_by_outlier function.
--filter-by-template-resolution=FILTER_BY_TEMPLATE_RESOLUTION
Boolen option [0/1] that control filetering results
with filter_by_template_resolution function.
--filter-by-alignment-length=FILTER_BY_ALIGNMENT_LENGTH
Boolen option [0/1] that control filetering results
with filter_by_alignment_length function.
New things since last release
This is the first public release in Rosetta3
- Supports the modern job distributor (jd2).
- Support for constraints .