I want to make a protein-protein docking. There are 19 proteins.
When I input the input parameters, it raise some error:
Request Entity Too Large The data value transmitted exceeds the capacity limit.
What should I do to solve this? Are there any suggestions for this situation?
How large is your system?
Can you share (e.g. via email) your input data?
Also modelling such large assemblies will only make sense if you have rather well defined data to drive the docking.
Ideally the information should be chain-specific (i.e. you should have some pair-specific information).
Defining active residues that would interact with all other molecules will be very inefficient and computationally demending.
Thank you.
I send a e-mail to a.m.j.j.bonvin@uu.nl, and my e-mail address is menglingshen@pku.edu.cn. Looking forward for your reply. Thanks a lot.
Hi there
It looks like you hit a technical limitation in our backend.
Docking some large assemblies will not make much sense unless you have some really good data…
You can of course try to run things on your side using a local installation of haddock2.5 or haddock3
Also looking at your system, it seems like it comes out of AlphaFold.
Why do you want to dock it as you have already an assembly?
If you just want to refine it, you can use the refinement interface:
https://rascar.science.uu.nl/haddock2.4/refinement/1
This seems to work with your system (submitted as one PDB file)
Thanks for your reply,
In fact, we have some cross-link mass spectrometry data.
After inspection, some of these cross-links cannot be satisfied by the existing structures. Therefore, we hope to use HADDOCK to explore whether there may be other structures.
Can this be achieved through HADDOCK?
You can indeed define cross-links - we have several tutorials about this, e.g.:
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Integrative modelling of the apo RNA-Polymerase-III complex from MS cross-linking and cryo-EM data |
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HADDOCK2.4 tutorial for the use of MS crosslink data to guide docking |
But to limit the computing requirements it might be best to limit your modelling to the parts that do not satisfy the cross-links.
And remove any disordered regions
