search

Discngine / fpocket

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).
MIT License
299 stars 62 forks source link

dpocket on apo-structures #102

Open fgentile89 opened 1 year ago

fgentile89 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

Thank you! That would certainly help a lot

ClaraVanM commented 8 months ago

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?