ProLIF: a library to encode molecular interactions as fingerprints

Table 2 Interactions currently available in ProLIF

Interaction	Ligand^a	Protein^a	Distance (Å)	Angle (deg)
Anionic	Anion	Cation	≤ 4.5
Cationic	Cation	Anion	≤ 4.5
CationPi	Cation	Aromatic	(+)-ctd ≤ 4.5	\(\langle \overrightarrow{n}, \overrightarrow{ctd\cdots (+)}\rangle \in \left[0, 30\right]\)
PiCation	Aromatic	Cation	(+)-ctd ≤ 4.5
PiStacking	Aromatic	Aromatic	ctd–ctd ≤ 6.0	\(\langle \overrightarrow{n}, \overrightarrow{n}\rangle \in \left[0, 90\right]\)
PiStacking	Aromatic	Aromatic	min ≤ 3.8
EdgeToFace	Aromatic	Aromatic	ctd–ctd ≤ 6.0	\(\langle \overrightarrow{n}, \overrightarrow{n}\rangle \in \left[50, 90\right]\)
EdgeToFace	Aromatic	Aromatic	Min ≤ 3.8
FaceToFace	Aromatic	Aromatic	ctd–ctd ≤ 4.5	\(\langle \overrightarrow{n}, \overrightarrow{n}\rangle \in \left[0, 40\right]\)
FaceToFace	Aromatic	Aromatic	min ≤ 3.8
HBAcceptor	HBAcceptor	HBDonor	D–A ≤ 3.5	\(\langle \overrightarrow{HD}, \overrightarrow{HA}\rangle \in \left[130, 180\right]\)
HBDonor	HBDonor	HBAcceptor	D–A ≤ 3.5
XBAcceptor	XBAcceptor	XBDonor	X–A ≤ 3.5	\(\langle \overrightarrow{XD}, \overrightarrow{XA}\rangle \in \left[130, 180\right]\)
XBDonor	XBDonor	XBAcceptor	X–A ≤ 3.5	\(\langle \overrightarrow{AX}, \overrightarrow{AR}\rangle \in \left[80, 140\right]\)
MetalAcceptor	Ligand	Metal	≤ 2.8
MetalDonor	Metal	Ligand	≤ 2.8
Hydrophobic	Hydrophobic	Hydrophobic	≤ 4.5

(−) anion; (+) cation; ctd centroid of the aromatic ring; min minimum value in the distance matrix between both aromatic rings; n normal to the aromatic ring plane; D hydrogen/halogen bond donor; A hydrogen/halogen bond acceptor; H hydrogen atom; X halogen atom; R atom linked to a halogen bond acceptor
^aAlthough “ligand” and “protein” are used here, all the listed interactions can be applied to any molecular complex (protein–protein, DNA–protein…etc.)

ISSN: 1758-2946