dpocket on apo-structures

[fgentile89]

Hi,
we are interested to use dpocket to calculate binding site descriptors of various apo forms of a protein (for which we have also the holo form). It is a bit unclear how to run dpocket on apo forms (while it seems clear how to do that for tpocket). Is this something that is possible to do with the most recent version?

Thanks in advance

Francesco

[pschmidtke]

Right now that's not that easy to do, you'd have to provide a list of residues or so to track a zone of interest somehow or define it as an explicit pocket.

This request might of interest for other types of applications as well, like general epitope predicton / detection.
Will add this as enhancement request to a major release.

[fgentile89]

Thank you! That would certainly help a lot

[ClaraVanM]

If I understand correctly, any point can be added to the pdb file as an HETATM line and used as the ligand of interest. dpocket will output a file with descriptors for all found pockets anyways?