Greetings all.
I’m preforming an Antibody-Antigen Docking assay using the HADDOCK web portal, but I would like to use a PDB containing a series of structures of the antibody obtained via MD simulation with GROMACS (specifically the centroids of each cluster after clustering the MD structures) as input. For that matter, I have changed the numbering of the structures in the PDB file so that there are not duplicated residue numbering, but keeping each structure as a different chain.
According to the previous, do I have to do something else to perform the docking to make sure that all the antibody structures in the PDB file are taken into account for the docking with the antigen?
Thanks in advance.
For this you should create an ensemble PDB file, with consistent numbering and chainIDs - meaning all models should have the same residue numbering and chainIDs. This is the same format used in the PDB database to represent NMR ensembles for example, using MODEL / ENDMDL statements.
It can be generated easily for example using our pdb_mkensemble command from our PDB-tools software (or web service).
See for example: https://www.bonvinlab.org/education/molmod_online/docking/#preparing-the-structures-for-the-docking-calculation
Thanks for the advice and directions, I’ll make sure to do this for my run.