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Commonly used protein pocket/cavity prediction tools

Tool Description Link
CASTp Computed Atlas of Surface Topography of proteins (CASTp) provides pockets located on protein surfaces and voids buried in the interior of proteins. CASTp
DEPTH Depth measures the closest distance of a residue/atom to bulk solvent. DEPTH
DogSiteScorer An automated pocket detection and analysis tool based on support vector machine, which uses calculated size, shape and chemical features of automatically predicted. DogSiteScorer
fpocket A high performance protein pocket (cavity) detection algorithm based on Voronoi tessellation. fpocket
GHECOM A program for finding multi-scale pockets on protein surfaces using mathematical morphology. GHECOM
LIGSITEcsc An automatic detection of pockets on protein surface using the Connolly surface and the degree of conservation. LIGSITEcsc
PDBinder A bioinformatic tool for the prediction of small ligand binding sites, which compares a query protein against a library of binding and non-binding protein surface regions derivative from the PDB. PDBinder
SiteHound SiteHound finds protein regions that are probable to interact with ligands by computing interactions between a chemical probe and a protein structure. SiteHound
CavityPlus A web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction CavityPlus

Souce: NovoPro    2019-05-10