TRAPP druggability - TRAnsient Pockets in Proteins

A pocket descriptor, D^s, for a particular property s is computed as

The descriptor d^s_ijk in each grid vertices' ijk for the pocket function ρ(ijk) is computed as

The 0.6 found in the equation corresponds to the default value of the iso-value used for pocket identification.

More information regarding this parameter can be found here.

R = 3Å (angstroms) is the interaction distance and the region of ρ(ijk) ϵ[0:0.6], which describes the pocket layer where a protein-ligand bond can be formed if an atom of the ligand is placed in this position.

Fig.1: Illustration of the computation procedure. The region defined by a pocket distribution value of ρ(ijk) ϵ[0:0.6] is shown in gray and the protein is colored in blue. Positions of several atoms of the type s are illustrated by red crosses and their interaction regions are indicated by dashed red lines (of the radius R). The value of 2 is assigned to the pocket descriptors in the vertices 1 and 3, d^s₁ and d^s₃ (because of the contact with two atoms of type s); d^s₂= 1.

This table describes the residue and atom type that is associated with each descriptor.

Descriptors	Residue Type	Atoms Type
Positive Residues (Pos.Res.)	HIS	ND1
	LYS	NZ
	ARG	NH1
	ARG	NH2
Negative Residues (Neg.Res.)	GLU	OE2
Negative Residues (Neg.Res.)	ASP	OD2
Hydrophobic Residues (Hydrophobic Res.)	VAL, ILE, LEU, MET, PHE, TRP, CYS	All heavy backbone atoms
Aromatic Residues (Aromatic Res.)	PHE, TRP, TYR, HIS	All heavy backbone atoms
Polar Residues (Polar Res.)	GLN, ASN, HIS, SER, THR, TYR, CYS, MET, TRP	All heavy backbone atoms
H-bond Donors	ARG	NE, NH1, NH2
	GLN	NE2
	HIS	ND1, NE2
	LYS	NZ
	SER	OG
	THR	OG1
	TRP	NE1
	TYR	OH
H-bond Acceptors	ASN	OD1
	ASP	OD1, OD2
	GLN	OE1
	GLU	OE1, OE2
	HIS	ND1, NE2
	SER	OG
	THR	OG1
	TYR	OH

Description of contact residues