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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
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On 6cs2 pockets on chain D are not detected #113

Closed pschmidtke closed 7 months ago

pschmidtke commented 8 months ago

To Reproduce Steps to reproduce the behavior: fpocket -f 6cs2.pdb

Expected behavior I'd expect to have at least a few pockets on chain D, but. I don't

pschmidtke commented 7 months ago

Happens because chain D is involved in collective motion versus the rest of the structure. the default fpocket behaviour filters by differences in bfactor vs average. Here this chain gets filtered out. The bfactor filtering is now changed to very local environments (4 atoms of an alpha sphere) -> standard deviation is computed and compared to the range of the b factors of the full structure (divided by 4) - good enough approximation for now IMO.

Likely reference results (number of pockets might change on some structures) - updating them