Dear HADDOCk user,
I would like to dock 6 molecules.
For this I have to use the multibody docking interface.
I used to dock earlier just two proteins, where the option of specification of active sites (which I defined by CPORT) was given.
I have experimental results from cross-linking. These I usually fed in as TBL file as unambigous restraints.
Is this a problem if the active sites are not defined the ambigous ones.
I appreciate every comment very much
best
Zsuzsi
Dear Zsuzsi,
If you have experimental results coming from crosslinking, you should indeed pass them to HADDOCK as unambiguous distance restraints in the TBL format. Provided you have enough of them to limit the sampling, there is no need to add any other restraints to your system.
If the cross-links are not enough to ensure a good compactness of your models (all molecules in contact in your system), you may want to use both center of mass restraints and unambiguous distance restraints
Best,
Adrien
Dear Adrien,
Many thanks for your answer.
It means I do not need to generate AIR files for multibody docking.
just to submit at the restraints the TBL file with the restraints of the different segIDs A-F
May be you can answer my second question:
Can I add intraprotein distances in this list as well? For refinement of the individual molecules?
Greetings
Zsuzsi from sunny Vienna
It means I do not need to generate AIR files for multibody docking.
just to submit at the restraints the TBL file with the restraints of the different segIDs A-F
Indeed, provided you have enough Xlinks. Otherwise, I would advise you to also turn on center of mass restraints to favor compactness of the solutions.
Can I add intraprotein distances in this list as well? For refinement of the individual molecules?
Yes you can. The TBL format is rather flexible and you can mix intra- and inter-molecular restraints. If needed, you can use the unambiguous, the ambiguous and the hydrogen bonds restraints fields to provide your TBL restraints.
Best,
Adrien