Modeling the structure of camel single domain antibody

This topic has 1 reply, 1 voice, and was last updated 7 years ago by Anonymous.

Viewing 1 reply thread

Author

Posts
- January 8, 2018 at 8:34 am #2826
  Anonymous
  I am now interested in modeling the structure of camel single domain antibody and find that an algorithm was implemented a algorithm in Rosetta in 2011 (https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d6/d32/camelid_modeler_protocol.html). The “Document for CAmelid application” (https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d6/d32/camelid_modeler_protocol.html) mentioned some file for running the protocol, e.g.：
  
        ~/antibody/scripts/rampaths.txt
  
       ~/antibody/scripts/utilities.txt
  
       ~/antibody/scripts/utilities.txt
  
  I have installed rosetta_src_2017.08.59291_bundle in my computer. However, the above files don’t exit in this Rosetta package. Could you tell me where I can find them?
  
  Then I turned to the Rosetta text directory. There is a “antibody_H3_camelid directory” in the “rosetta/main/rosetta_tests/integration/tests” path. I ran the follow command in this “antibody_H3_camelid directory” directory:
  
        antibody_H3.linuxgccrelease @flags -database /app/rosetta_src_2017.08.59291_bundle/main/database/ -run:constant_seed -nodelay
  
  and it generated a FR02_H_0001.pdb file. Is it the fine modeling result for the input sequence? There is a FR02_H.pdb file in the “input” subdirectory of the “antibody_H3_camelid directory” directory, so I guess the FR02_H_0001.pdb is more likely a relaxation or minimization result of the FR02_H.pdb . Without a detailed explanation or tutorial, I can hardly understand how to run the test. Could you provide me with one such tutorial?
  
  I would be very grateful if you could help.
- January 8, 2018 at 8:55 am #13979
  Anonymous
  The following is the reply from Jeliazko:
  
  I’d be glad to help. I’m in the process of updating our camelid modeling protocol, so there is no concrete manual. So, to get started, I would recommend you download a version from Dec. 2017 — it includes an update that permits camelid modeling and a crucial bug fix. Next, compile it (./scons -j<# of processors> mode=release bin), which should generate the antibody executable in $ROSETTA/main/source/bin/. Alternatively, you may be able to download a version with pre-compiled executables. Now, you can homology model camelid antibodies by supplying a fasta file with two lines: the first should read “>heavy” and the second should be the amino acid sequence. The command line to run modeling is: “/path/to/antibody -vhh_only -antibody:n_multi_templates 1”. After about 20 minutes of runtime, this should result in a homology model where a homologous FR and homologous CDRs were found by BLAST search against a database and assembled. The final step is to run de novo modeling of the CDR H3 loop. This is done with the antibody_H3 executable and instructions on how to run this are analogous to the ones reported here: https://www.biorxiv.org/content/early/2016/08/16/069930.article-metrics
  
  Let me know if anything is unclear or you need more help. Camelid antibody modeling with the latest version of Rosetta is still under active development.
  
  -Jeliazko
Author

Posts

Viewing 1 reply thread

You must be logged in to reply to this topic.