RosettaDock: questions about Fab file and constraints

[cmathisjhu-edu]

Hi,
some questions:

1- in an antibody-protein docking, is it possible to create a TFN constraint file, like the Fab file, also for the antigen?

2- Can you tell me exactly the correct format of a constraint file?
For example, if I want to exclude from the interface the residues 54-68, 74-78, 80 and 85-90 of the antigen (chain A), what axactly do I have to write? Is there some limitations on the number of the residues incorporated in this constraint?

Thanks

Luca

[Anonymous]

Please check the answer from Docking developers:
===
I guess its possible to assign a FAB file to the antigen as well. Assuming that the first partner is the antibody and the second partner is the antigen. First use the command line option -fab1 to point to the fab file of the antibody. Then create a similar file for the antigen. The format should be like the fab file for the antibody. All the residues in the fab file should match with that of the antibody.

Depending on whether you would like to have some interfaces at the interface and award bonuses. The details are as follows:
bad = { 1.5 }; // . or F
neutral = { 0.5 }; // N or 1
ok = { 0.45 }; // 2
good = { -0.0 }; // T or 3-9
bonus = { -0.5 }; // B

So if you would like to award a super bonus, you would annotate the residue with the letter B, for a normal bonus, you would annotate it as T and so on and so forth. The character following the sign “//” is indicative of the letter to be used to award bonuses or penalties.

Aroop

> Hi,
> some questions:
>
> 1- in an antibody-protein docking, is it possible to create a TFN constraint file, like the Fab file, also for the antigen?
>
> 2- Can you tell me exactly the correct format of a constraint file?
> For example, if I want to exclude from the interface the residues 54-68, 74-78, 80 and 85-90 of the antigen (chain A), what axactly do I have to write? Is there some limitations on the number of the residues incorporated in this constraint?
>
> Thanks
>
> Luca

[cmathisjhu-edu]

Thanks for the explanation.

I have another question:

IS IT POSSIBLE TO CHANGE THE VALUES OF THE BONUS AND PENALTIES AND
WHERE DO I HAVE TO GO TO CHANGE THEM?

Thanks

Luca

[Anonymous]

The values can be changed in the file “dock_fab.cc”.

Best,
Aroop

[Author]

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