Fpocket: An open source platform for ligand pocket detection

Abstract

Background: Virtual screening methods start to be well established as effective approaches to identify hits, candidates and leads for drug discovery research. Among those, structure based virtual screening (SBVS) approaches aim at docking collections of small compounds in the target structure to identify potent compounds. For SBVS, the identification of candidate pockets in protein structures is a key feature, and the recent years have seen increasing interest in developing methods for pocket and cavity detection on protein surfaces.

Na + coordination at the Na2 site of the Na + /I − symporter

“…The final model of NIS was analyzed for cavities that might correspond to ion-binding sites using the programs Voidoo (Uppsala Software Factory), Cavenv (CCP4 suite), and fpocket (67). Besides the Na2 site, the program identified an additional major cavity that structurally coincides with the locations of the vSGLT and LeuT substrates previously determined by X-ray crystallography.…”

Computational modelling of the binding of arachidonic acid to the human monooxygenase CYP2J2

“…In addition, the inclusion of heme itself could alter the results significantly due to the large volume occupied by this cofactor. Indeed, calculations of the active site volume using fpocket [43] or the cavities analysis from In addition to the residues mentioned above, a channel to the active site was lined by a network of mostly hydrophobic residues, creating a favourable environment for the long non-polar AA chain. The following ten residues were in contact with the substrate in all 20 poses from IFD: Thr114, Phe121, Ile127, Asp307, Phe310, Ala311, Glu314, Thr315, Ile376 and Ile487, while there were several others that appeared in at least half the poses (e.g.…”

Untitled

“…To that extent, usual CAAD techniques can be useful to estimate the druggability and the effects of small molecules on IDP interactions [10,34,71,72]. These methods analyze the cavities over static structures coming from experiments or simulations such as DrugPred [73], Cavity [74] or fpocket [75], or coupled to MD simulations and calculate the druggability "on-the -fly", such as the recently developed JEDI [76].…”