is protein preparation required before submission to HADDOCK2.4 server?
What do you mean by that exactly?
It also all depends where you protein is coming from?
if it is homology model? do we need to prepare it by adding charges/hydrogen before submission to HADDOCK?
and if the protein structure is downloaded from PDB ?
No need to add missing atoms. HADDOCK will deal with that.
When using PDB files, make sure to remove any junk (e.g. small molecules from the crystallisation buffer, water, unneeded chains…). Never use blindly a PDF file. Look at its content!
Structure preparation is covered in our Best Practices Guide, please have a look at it and let us know if there are still any questions;
thank you for the clarification.