The protein-protein docking pose I got from the easy interface had significant deviation from the crystal structures (as my inputs). Is there a way to specify in the expert interface so there is minimal change to the crystal coordinates (rigid docking)? I compared HADDOCK with CLUSPRO, and I found CLUSPRO poses are more like rigid docking.
Well… cluspro is a rigid body docking programme - haddock allows for flexibility.
Define further what you mean by significant changes…
Finally there is little point in performing bound docking except for benchmarking and validation.
At the expert level in Haddock you can define molecules as rigid.
By “significant changes” I mean backbone and also side chains are different compared to the crystal structure. For example, one of the docking partner contains 3 chains, there are inter-chain H-bonds that are broken in the results. It’s true allowing flexibility this is what you would get, but for the moment I prefer rigid docking or at least the backbone should stay rigid.
I am not doing bound docking. I took protein A from crystal 1 and dock it onto protein B in crystal 2. The binding of A to B is not known.
Could you elaborate on how to do rigid docking using Haddock? Is it enough to leave blank the semi and full flexible segments, specify manual definition for flexible segment, and keep the rest as default?
In the expert interface set the semi flexible segment setting to manual for each protein and let all fields blanc
Also if you have multiple chains in one protein, make sure there is no overlap in residue numbering and tell haddock to use all chains
I did as you suggested but got error message
There was an inconsistency in your data
You defined manual semi-flexible segment specification, but you did not define any segments."
Is this expected?
It seems you discovered a “feature” that was present in the 2.1 version of the HADDOCK server and disappeared in the 2.2.
We had perviously as option for the semi-flexible segments: none, which is currently not available in the 2.2 version.
A simple fix - currently testing to make sure it works.
Will let you know once implemented in the production version.
Sorry for that.
Do you have an estimate when this is gonna be done?