Table 1.
Attributes of interaction
| Attribute type | Attribute name | Computational tools used |
|---|---|---|
| Binding site descriptors | Pocket volume |
|
| Number of alpha spheres | ||
| Mean alpha sphere radius | ||
| Proportion of apolar alpha spheres | ||
| Mean local hydrophobic density | ||
| Hydrophobicity scores | ||
| Volume score | ||
| Charge score | ||
| Proportion of polar atoms | ||
| Alpha sphere density | ||
| Max. distance between COM and alpha sphere | ||
| Max. theoretical shape complementarity | ||
| Observed shape complementarity | ||
| Normalized shape complementarity | ||
| Binding site environment and binding energetics | Autodock score |
|
| Electrostatic score | ||
| Hydrogen bond score | ||
| van der Waal score | ||
| Desolvation score | ||
| Torsional score | ||
| Average methyl probe (CMET) interaction energy | ||
| Total CMET interaction energy | ||
| Total CMET interaction grids | ||
| Total CMET interaction clusters | ||
| Average phosphate probe (OP) interaction energy | ||
| Total OP interaction energy | ||
| Total OP interaction grids | ||
| Total OP interaction clusters | ||
| Average hydroxy probe (OA) interaction energy | ||
| Total OA interaction energy | ||
| Total OA interaction grids | ||
| Total OA interaction clusters | ||
| Average aromatic probe (CR1) interaction energy | ||
| Total CR1 interaction energy | ||
| Total CR1 interaction grids | ||
| Total CR1 interaction clusters | ||
| Ligand–protein contacts | Hydrogen bonds |
|
| Aromatic | ||
| Hydrophobic | ||
| Destabilizing | ||
| Donor water molecules at the binding site | ||
| Acceptor water molecules at the binding site |
All the attributes that are calculated for each of the interactions present in the database along with the computational tools used to derive them have been listed in this table.