. Author manuscript; available in PMC: 2022 Mar 8.

Published in final edited form as: J Chem Inf Model. 2020 Sep 10;60(9):4200–4215. doi: 10.1021/acs.jcim.0c00411

Table 3:

Affinity prediction performance on PDBbind Core (N=280) for a variety of models.

Model	RMSE	R
Def2018 Refined Crystal	1.50	0.73
Def2018 Refined	1.50	0.72
Def2018 General	1.38	0.79
Def2018 General Ensemble	1.37	0.80
Dense General	1.49	0.73
Dense General Ensemble	1.35	0.79
Pafnucy²⁴^*	1.42	0.78
KDeep^23†	1.27	0.82
RF Score^16‡	1.39	0.80
1D2D CNN^29†	1.64	0.848
Vina	2.22	0.41

Train: PDBbind General and Refined v2016 crystal structures (N=11,906). Removed Nucleic Acid+Protein, Protein+Protein, and Nucelic Acid+Ligand from all sets. Test: remaining Core set (N=290).

^†

Train: PDBbind Refined v2016 crystal structures (N=3767). Test: PDBbind Core set crystal structures (N=290)

^‡

Train: PDBbind Refined v2007 crystal structures (N=1300). Test: PDBbind Core set crystal structures (N=195)