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).
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dpocket-pocket volume reduces in the presence of HETATMs #101
I am trying to calculate the volume of the binding pocket for a protein using dpocket in the presence and absence of lipids like POPC and POPE. The lipids are outside the binding site but within 4 angstroms of the ligand so I expected an increase in the pocket volume since I am using the explicit (-E) flag to consider all atoms within 4 angstroms of the ligand. However, the pocket volume is decreased in the presence of the lipids. For example, without the lipids, it is 2000 but in their presence it's 1600. I expected it to at least remain the same and not decrease except I am missing something here. I tried to'trick' the algorithm and changed the names to another name in the protected HETATM list to see if the problem was as a result of them not being considered by the algorithm but the results remained the same. How can I solve this?
I am trying to calculate the volume of the binding pocket for a protein using dpocket in the presence and absence of lipids like POPC and POPE. The lipids are outside the binding site but within 4 angstroms of the ligand so I expected an increase in the pocket volume since I am using the explicit (-E) flag to consider all atoms within 4 angstroms of the ligand. However, the pocket volume is decreased in the presence of the lipids. For example, without the lipids, it is 2000 but in their presence it's 1600. I expected it to at least remain the same and not decrease except I am missing something here. I tried to'trick' the algorithm and changed the names to another name in the protected HETATM list to see if the problem was as a result of them not being considered by the algorithm but the results remained the same. How can I solve this?