Table 3.

Summary of binding affinity prediction methods

Binding affinity prediction
Method	Architecture	Features used	Benchmark against	Year	Code/Webserver
K DEEP	3D-CNN (variant of SqueezeNet)	Atomic descriptors for local interactions	RF-Score, X-Score, and CyScore	2018	www.playmolecule.org/kdeep/
Pafnucy	3D-CNN	Atomic descriptors for local interactions	X-Score, RF-Score, ChemScore, ChemPLP, PLP1, and G-Score	2018	https://gitlab.com/cheminfIBB/pafnucy
DeepAtom	3D-CNN (variant of ShuffleNet)	Atomic descriptors for local interactions	Pafnucy and RF-Score	2019	Not publicly available
OnionNet	2D-CNN	Atomic descriptors for local and non-local interactions	Pafnucy, RF-Score, and K DEEP	2019	http://github.com/zhenglz/onionnet/
AK-Score	3D-CNN ensemble-based (variant of ResNet)	Atomic descriptors for local interactions	AK-Score single network and K DEEP	2020	Not publicly available
RosENet	3D-CNN (variant of ResNet)	Molecular energies from Rosetta and atomic descriptors	K DEEP, Pafnucy, and OnionNet	2020	https://github.com/DS3Lab/RosENet/tree/master/models