Table 1. Our test set is comprised of proteins for which structures have been solved both alone and in complex with a small-molecule inhibitor bound to the protein interaction site.

Protein	Partner	Number of residues	Number of residues used in simulations	Deep pocket volume from unbound protein structure (Å3)	Deep pocket volume from protein-protein complex (Å3)	Deep pocket volume from inhibitor-bound complex (Å3)	Deep pocket volume from conformations generated via biased simulations (the 5% with lowest energy) (Å3)	Affinity of most potent known inhibitor (nM)
MDM2	p53	492	119	129	150	201	194	80
ZipA	FtsZ	328	139	91	166	61	92	12,000
Bcl-xL	Bak	233	141	200	377	342	210	0.5
XIAP	SMAC	497	117	158	27	40	323	67
IL-2	IL-2R	153	128	38	38	38	177	60
HPV E2	HPV E1	367	193	93	92	132	129	40
FKBP12	Tbeta1-R	108	107	90	124	145	116	7