Table I.

Performance of our docking and scoring method in CAPRI rounds 22–28.

Targeta	Complexb	Typec	Bio.d Info.	Predicting				Scoring
				fnat (%)	Lrmsd (Å)	Irmsd (Å)	accuracye	fnat (%)	Lrmsd (Å)	Irmsd (Å)	accuracyf
46	Mtq2/Trm112	H/H	–	0.040	19.646	10.356	0	0.406	7.621	3.395	1*
47	E2/IM2	U/U	Y	0.821	0.865	0.554	10***	0.821	0.904	0.535	10***
48	T4moH/T4moC	U/U	Y	0.375	3.921	1.653	8/1**	–	–	–	–
49	T4moH/T4moC	U/U	Y	0.312	5.678	2.177	4*	0.500	5.593	1.790	7/2**
50	HA/HB36.3C	U/H	Y	0.673	9.618	2.239	1*	0.571	5.650	1.912	2/1**
51	GH5-CBM6/CBM13/Fn3	U/H/U	–	0.000	17.052	11.562	0	0.241	20.501	3.483	1*
53	REP-4/REP-2	U/H	–	0.096	13.504	3.935	0	0.288	5.321	2.517	1*
54	NCS/REP16	U/H	–	0.040	18.315	7.831	0	0.040	12.231	5.397	0
57	BT-4661/heparin	U/U	Y	0.706	3.216	1.369	2/1**	–	–	–	–
58	SalG/PliG-Ec	U/U	Y	0.275	3.602	1.807	3*	–	–	–	–

^aT52 was cancelled and Targets 55 and 56 are for binding affinity prediction which are not listed in this table.

^bThe first one is assigned as the receptor, and the second one as the ligand.

^cThe symbol “B” stands for the bound experimental structure, “U” for the unbound experimental structure, and “H” for the homology-modeled structure.

^d“Y” represents that valid biological information was available for the binding site, “–” represents that no or little useful biological information was available.

^eThe accuracy is categorized by three parameters following the CAPRI criteria:^7,8 The percentage of the native residue-residue contacts (f_nat), the ligand RMSD (L_rmsd), and the interface RMSD (I_rmsd). “***” stands for high-accuracy, “**” for medium-accuracy, “*” for acceptable accuracy, and “0” for no correct prediction, respectively. For example, “8/1***” means that among 10 submitted binding modes for CAPRI, eight modes have at least acceptable accuracy, and one of these eight has high accuracy (***).

^fThere were no scoring experiments for Targets 48, 57, and 58.