Table 3.

Comparison of gEDES, NeuralPLexer, and AlphaFold3 performances in reproducing native-like conformations of the complexes between AK and the four ligands investigated in this work. See caption of Table 2 for further details.

		AP5	AMP	ADP	GCP
Autodock-gEDES	RMSDlig/BS [Å]	2.2/2.2 (2)	2.1/3.1 (7)	0.9/1.1 (1)	1.8/2.3 (10)
	F nat	0.79	0.74	0.86	0.91
HADDOCK-gEDES	RMSDlig/BS [Å]	1.6/2.1 (1)	1.7/2.7 (193)	0.6/1.4 (1)	1.7/2.0 (11)
	F nat	0.82	0.67	0.88	0.86
NeuralPLexer	RMSDlig/BS [Å]	1.6/1.9 (1)	1.3/2.1 (1)	1.0/1.8 (1)	-*
	F nat	0.89	0.90	0.77	-*
AlphaFold3	RMSDlig/BS [Å]	-†	0.9/1.3 (1)	0.3/0.6 (1)	-†
	F nat	-†	1	1	-†

^*NeuralPLexer was unable to correctly reproduce the conformation of the protein and of the BS (minimum RMSD ~5.9 Å), as well as native-like poses of GCP (RMSD_min ~ 3.8 Å, F_nat = 0.50)

^†The AlphaFold3 server (https://alphafoldserver.com/) allows in the current implementation to predict the binding of only a few ligands, including AMP and ADP.