. Author manuscript; available in PMC: 2020 Jun 11.

Published in final edited form as: J Chem Inf Model. 2009 Dec;49(12):2801–2812. doi: 10.1021/ci900289x

Table 3.

Performance of the Nine pK_a Prediction Programs Using a Set of 261 Protonation Sites, Sorted Alphabetically by Program Name

program	number handled	predicted excellently (AD^a ≤ 0.1)	predicted well (0.1 < AD ≤ 0.5)	predicted poorly (1.0 < AD ≤ 2.0)	predicted awfully (AD > 2.0)	r²	MAD^b
ACD/pK_a DB	261	64	121	17	10	0.908	0.478
ADME Boxes	256	95	102	16	7	0.944	0.389
ADMET Predictor	261	40	119	28	18	0.837	0.659
Epik	257	30	87	64	23	0.802	0.893
Jaguar	193	24	38	36	40	0.579	1.283
Marvin	261	39	91	57	22	0.763	0.872
Pallas pKalc	259	48	105	32	26	0.803	0.787
Pipeline Pilot	252	77	74	46	24	0.757	0.769
SPARC	243	30	96	45	12	0.894	0.651

AD: absolute deviation.

MAD: mean absolute deviation.