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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MDpocket giving out volume as zero for some snapshots in the trajectory #138
MDpocket isn't capturing pockets in some snapshots
Using reference pdb of a descriptor pocket, I am trying to analyse the snapshos in my MD trajectory. But I have been getting similar output in the mdpout_descriptors.txt where some snapshots are showing the pocket volume and other data sets, but some are simply showing 0.
This means that with the default fpocket parameters for typical small molecule binding site detection you don't find you binding site anymore. Is the volume rather low or the surface very shallow?
pschmidtke
commented
3 months ago
MDpocket isn't capturing pockets in some snapshots Using reference pdb of a descriptor pocket, I am trying to analyse the snapshos in my MD trajectory. But I have been getting similar output in the mdpout_descriptors.txt where some snapshots are showing the pocket volume and other data sets, but some are simply showing 0.
mdpout_descriptors.txt