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Authors: 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).

Code for Reading Constraints

  • Application source code:

    rosetta/rosetta_source/src/apps/pilot/jianqing/antibody_model_CDR_H3.cc

  • Main mover source code:

    rosetta/rosetta_source/src/protocols/antibody2/AntibodyModelerProtocol.cc.cc

  • To see demos of some different use cases see integration tests located in

    rosetta/rosetta_tests/integration/antibody_protocol_* (antibody_protocol_using_KIC_loop_mover, antibody_protocol_using_CCD_loop_mover).

To run Rosetta3Antibody, type the following in a command line:

[path to executable]/antibody_model_CDR_H3.[platform|linux/mac][compile|gcc/ixx]release –database [path to database] @options

Note: these demos will only generate one decoy. To generate a large number of decoys you will need to add –nstruct N (where N is the number of decoys to build) to the list of flags.

References

We recommend the following articles for further studies of RosettaDock methodology and applications:

  • B. D. Weitnzer*, J. R. Jeliazkov*, S. Lyskov*, N. Marze, D. Kuroda, R. Frick, J. Adolf-Bryfogle, N. Biswas, R. L. Dubrack Jr, & J. J. Gray, "Modeling and docking of antibody structures with Rosetta," Nature Protocols 12, 401–216 (2017)

  • 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

Determine the structure of antibody homology models by combining VL-VH docking (using docking protocol) and H3 loop modeling (loop modeling protocol ).

Input

  1. starting structure, mandatory (e.g. input.pdb)
    • a). The input antibody file needs to be Chothia numbered.
    • b). It can be an crystal structure
    • c). or homology model (check Work Flow and Graft Protocol)

Flags

Sample command line (as of May 17th, 2020): antibody_H3.macosclangrelease @flags.

flags: 

# input grafted model
-s grafting/model-0.relaxed.pdb

# recommended number of structs
-nstruct 1000 

# constraints are enabled by default, so flags are shown just to indicate that they can be turned off
# recommended as kink is present in 90% of Abs and as VH-VL Q-Q is present in 808%
-antibody:h3_loop_csts_lr true
-antibody:h3_loop_csts_hr true
-antibody:auto_generate_h3_kink_constraint true
-antibody:constrain_vlvh_qq true
-constraints:cst_weight 1.0

# standard settings, for packages used by antibody_H3
-ex1
-ex2
-extrachi_cutoff 0

# necessary if running multiple procs w/o MPI
-multiple_processes_writing_to_one_directory 

# specify output file
-out:file:scorefile H3_modeling_scores.fasc 

# specify output folder
-out:path:pdb H3_modeling

Detailed Description of Flags (may not have been included above):

-antibody::snugfit

  • Description:

    • Optimize VL-VH orientational via L-H docking

  • options:

    • true (default) or false
-antibody:h3_loop_csts_lr true
-antibody:h3_loop_csts_hr true
-antibody:auto_generate_h3_kink_constraint true
-antibody:constrain_vlvh_qq true
  • Note all these flags are true by default as they implements constraints to known antibody motifs. The kink is observed in ~90% of antibody CDR H3 loops and the VL-VH QQ h-bond is observed in ~80% of structures.

  • Description:

    • a). "-antibody:h3_loop_csts_lr" enables constraints in the low-resolution stage. Can be manually specified constraints or automatically generated ones.
    • b). "-antibody:h3_loop_csts_hr" enables constraints in the high-resolution stage. Can be manually specified constraints or automatically generated ones.
    • c). "-antibody:auto_generate_h3_kink_constraint" sets up the correct weights and constraints to emulate the kink observed in 90\% of all antibodies (see Weitzner and Gray, J. Immunol. 2016 paper).
    • d). “-antibody:constrain_vlvh_qq” the VH--VL Q--Q hydrogen bond(s) that occur(s) in ~0\% off all antibodies.
    • e). "-constraints:cst_file ./constraint_file" specifies constraints. Q-Q bond constraints used to be manually specified as (for example): 
      AtomPair CD 38L CD 39H LINEAR\_PENALTY 4.1 0 0.4 400

  • Options:

    • true or false
    • local of the constraint file

Additional Description of constraint file:

AtomPair CD 38L CD 39H LINEAR_PENALTY 4.1 0 0.4 400 1. To constrain two GLN, one is on L chain, the other is on H chain, they form Hydrogen bond at the L-H interface 2. “CD” is the the carbon on GLN bonding to Nitrogen and Oxygen 3. 38L means L chain 38, and 39H means H chain 39. They are GLN forming hydrogen bond. 4. LINEAR_PENALTY potential, see details in constraint file 5. distance_constraint=4.1, well_depth=0, width=0.4, slope=400, see the details in constraint file.

FoldTree output

One antibody PDB structure with modeled H3 loop and optimized VL-VH orientation.

New things since last release

This is the first public release in Rosetta3

  • Supports the modern job distributor (jd2).
  • Support for constraints .

See Also