Hello,
i want to perform density driven docking of a protein-ligand complex.
The density was derived from cryo-EM experiments. The maps i have are all in the MRC file format.
I did not manage to convert them into the xplor format as used in the “protein-protein-em” example.
I wanted to ask what would be the best approach to this problem?
In principle for what you want to do (docking a small ligand) you only need the density part from the ligand.
Our shape-based protocol might be a better option for this. Check:
- P.I. Koukos, M.F. Reau and A.M.J.J. Bonvin. Shape-restrained modelling of protein-small molecule complexes with HADDOCK. J. Chem. Inf. and Mod. 61, 4807–4818 (2021). BioRxiv preprint available here.
And the following tutorial:
https://www.bonvinlab.org/education/HADDOCK24/shape-small-molecule/
As for the conversion to xplor format, did you try to use the em2xplor.py script provided in the EMtools directory (assuming you are using a local version of HADDOCK? (but again, in this case I would advice to convert your ligand density into a collection of beads and use the shape docking protocol.
Thanks for the answer!
Ill try the shape based approach, it sounds like it fits perfectly with my case.
I did not try em2xplor.py but i will for future problems.