2.3 Active site analysis of viral virulence factors
DoG Site Scorer, a web based tool (https://proteins.plus/), was used to
predict the possible binding sites in the 3D structure of spike
glycoprotein, viral nuclease and viral main protease. Predictions with
DoG Site Scorer were based on the difference of gaussian filter to
detect potential pockets on the protein surfaces and thereby splitting
them into various sub-pockets. Subsequently, global properties,
describing the size, shape and chemical features of the predicted
pockets were calculated so as to estimate simple score for each pocket,
based on a linear combination of three descriptors, i.e ., volume,
hydrophobicity and enclosure. For each queried input structure, a
druggability score between 0-to-1 was obtained. Higher the druggability
score, higher the physiological relevance of the pocket as potential
target (Volkamer et al., 2012).