Protein self-interaction/aggregation without known active residues

HADDOCK
1

I was going through the haddock webinar recently and if im not wrong, what i understand is that it’s necessary to input active and passive residues.

My work involves identifying protein hotspots that result in protein self-aggregation. As there is no literature on the particular residues that are involved in this process, im unable to input these active/passive residues.

I did notice that the webinar also mentioned something about protein-protein docking using solvent accessible surface area.
Is this available in haddock 2.2 or 2.4? Im not able to find the specific function in both.

Would appreciate it if anyone can point me in the right direction. Thanks!

2

HADDOCK does have an ab-initio mode in the form of either centre of mass restraints or random AIRs.
You will need expert or guru access for those.

And in that case you should increase the sampling, e.g. to 10000/400/400 for the various stages.

See also:

https://www.bonvinlab.org/software/haddock2.4/airs/#random-air-definition-ab-initio-mode
https://www.bonvinlab.org/software/haddock2.4/airs/#center-of-mass-restraints

3

Cool! Thanks for the links. Ill check them out and come back if i have further questions.