Pocket Descriptors

Comprehensive analysis of protein pocket properties and characteristics

After NanoShaper delivers the set of pockets of a protein, a further script is used to estimate the molecular DrugPred descriptors with minor modifications (the entrance area computed by NanoShaper is used as an additional descriptor).

Pocket Descriptors

Basic Geometric Properties

Fundamental measurements of pocket geometry and shape

vol
Pocket/cavity volume
Total volume of the pocket/cavity
area_b
Total surface area
Complete surface area of the pocket/cavity
area_e
Entrance area
Area of the pocket entrance
cness
Pocket/cavity compactness
Measure of pocket/cavity shape characteristics

Surface Properties

Hydrogen bonding and hydrophobic characteristics

Hydrogen Bond Donor Areas

dsa_t
Total donor surface area
Absolute donor surface area
dsa_r
Relative donor surface area
Normalized by total surface area
psa_r
Relative polar surface area
Sum of relative donor and acceptor areas (dsa_r + asa_r)

Hydrogen Bond Acceptor Areas

asa_t
Total acceptor surface area
Absolute acceptor surface area
asa_r
Relative acceptor surface area
Normalized by total surface area

Hydrophobic Properties

hsa_t
Total hydrophobic surface area
Total - (donor + acceptor areas)
hsa_r
Relative hydrophobic surface area
Normalized by total surface area

Amino Acid Composition

Distribution and occurrence of different amino acid types

paa
Polar amino acids
Relative occurrence in binding site
haa
Non-polar amino acids
Relative occurrence in binding site
maa
Multifunctional amino acids
Relative occurrence in binding site
caa
Charged amino acids
Relative occurrence in binding site
in_X
Individual amino acid incidence
Sum of surface areas surrounding each amino acid type X, relative to the binding site surface

Detailed Description

Surface Properties

Each pocket identified by NanoShaper is characterized by descriptors from Krasowski et al. (2011), along with the entrance area provided by NanoShaper. Binding site properties include hydrogen-bond donor and acceptor surface areas (dsa_t and asa_t), calculated around polar atoms.

Area Calculations

The hydrophobic surface area (hsa_t) is derived by subtracting the hydrogen-bond donor and acceptor areas from the total surface area. Relative descriptors (dsa_r, asa_r, and hsa_r) are computed by normalizing each by the total binding site surface area, with the relative polar surface area (psa_r) defined as the sum of dsa_r and asa_r. Finally, the compactness descriptor is used to characterize cavity shapes.

Amino Acid Properties

The remaining descriptors, related to amino acid composition, were calculated based on the occurrence of different amino acid classes grouped by their physicochemical properties. Moreover, the occurrence of each amino acid of type (in_X) is reported as descriptors, computed as the sum of all the surface areas surrounding the amino acid X.