RosettaAntibody

[Anonymous]

I have been using Rosetta for about a year now and have been interested in using RosettaAntibody for some time now. I have held off installing Rosetta++ in the hopes that RosettaAntibody would be included in the new 3.2 build. Does anyone know if this is the case, or will I still need to install Rosetta++ in order to access that algorithm without taking up space on the RosettaAntibody webserver?

[Anonymous]

Hi MPendleton,

Parts of RosettaAntibody have been ported to Rosetta3.2. There is a new camelid modeling tool that has been developed and extensively tested with Rosetta 3.2 (publication to appear in J. Immunology). However, the standard RosettaAb and SnugDock has not been tested in Rosetta3. We are currently in the process of benchmarking it, and also developing some OO-based tools for managing Ab information. Look for this hopefully in the 3.3 release! In the meantime, I would suggest using the RosettaAntibody server or the Rosetta2.x release for antibody modeling.

Jeff Gray

[snaigaga]

RosettaAntibody appears to be included in the Rosetta 3.3 release. However, one of the main scripts used to graft the CDRs on to the framework, ram_buildloop_wrapper.pl, includes several calls to the executable “rosetta.gcc”. As I understand it, rosetta.gcc is a Rosetta 2 executable, not a Rosetta 3 executable.

For example, the ram_buildloop_wrapper.pl script includes the line

system2(“$bin/rosetta.gcc aa $which_framework _ -antibody_modeler -nstruct $nstruct_grafting -quiet -l1 -l2 -l3 -h1 -h2 -graft_h3 -superimpose -deep 2 -use_pdb_numbering -ccd_closure -s $which_framework -native $pdbcode -find_disulf -norepack_disulf|tee rosetta$which_framework_grafting.logfile”) ;

Should I just use a Rosetta v 2 executable for these commands? Or is there a Rosetta 3 equivalent command that could be used here?

There are other scripts/files that don’t seem to be included with the Rosetta 3.3 distribution, such as:
paircutoffs (which is supposed to be in a place specified in paths.txt and does not appear to be in any sort of rosetta database directory)
$scripts_alt/extractres.pl
$docking_scripts/pdb_scripts/makefixdisulf.py

Should we just use the versions of these files that came with Rosetta 2?

[Anonymous]

Hi,

You are right, the executable “rosetta.gcc” is from Rosetta2. Although some of the original functions of RosettaAntibody were included in the Rosetta 3.3, they have not been well tested. At this moment, I would suggest you continue using Rosetta2. The Gray lab is currently refactoring the RosettaAntibody code. We will let the community know as soon as we release the new version.

For the demo of using the Rosetta2 based antibody docking protocol, please check:
https://svn.rosettacommons.org/source/trunk/RosettaCon2011/demos/antibody_docking/

Thanks,

Jianqing

[Author]

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