. Author manuscript; available in PMC: 2006 Aug 30.

Published in final edited form as: J Med Chem. 2005 Jun 2;48(11):3714–3728. doi: 10.1021/jm0491187

Table 4.

Characteristic L99A/M102Q Experimentally Tested Ligands and Decoys Scoring in the Top 10 000 Docking Hits and Their Ranks by Different Scoring Functions

		Ranking by scoring function^a
#	Ligands	D	S	F	PLP	PME	S*	K_d^b(μm)
1.		8	577	332	1200	1027	NA	NA
2		9	361	139	939	5642	NA	NA
3.		17	1244	1082	2041	2257	2175	156
4.		48	1336	701	3191	8796	NA	NA
5.		60	358	166	780	848	NA	100
6.		171	3278	3708	2640	1430	511	NA
7.		308	4738	3169	7045	6720	5371	159
8.		355	1100	708	1857	3676	3857	90.9
9.		417	821	942	421	4318	NA	NA
10.		536	3026	2085	5969	5280	NA	56
11.		606	561	419	1573	4731	3594	NA^c
12.		845	1185	1087	4285	4465	1214	NA
13.		979	1419	2765	1081	2017	751	NA
14.		1052	1067	1373	2956	7399	NA	NA
15.		1577	1495	1804	3132	2314	NA	NA
16.		2462	1503	1883	2197	1888	NA	NA
17.		2777	1380	734	5511	9286	NA	NA
18.		3557	2339	3144	2654	2550	1485	NA
19.		4277	1795	2541	4044	1403	81	NA
20.		4471	3808	3462	5322	4098	2649	NA
21.		4593	1150	1147	3436	374	111	NA
22.		5512	2034	1971	5544	2591	323	NA
1.		28	8531	6677	9212	9803	NA
2.		64	53	18	196	3553	NA
3.		137	4714	4188	2809	3791	5074
4.		152	1740	1876	2304	1323	2970
5.		198	1581	939	3271	1849	NA
6.		209	65	43	503	1449	2216
7.		1030	2248	3301	2456	4276	841
8.		1451	1600	2167	1585	1394	744
9.		3261	2908	3447	3057	2291	2446
10.		7018	3641	3743	5584	3668	1091

D = DOCK, S = ScreenScore, F = FlexX, and S* = SMoG (SMoG ranks are based on a ranking, which does not include halogenated compounds). Ranks in bold font indicate decoys, which rank in the top 500 for the respective scoring function.

Experimentally determined K_d values.³⁵

ΔT_m =2.6 °C. A full list of L99A/M102Q ligands and decoys may be found in the Supporting Information and at http://shoichetlab.compbio.ucsf.edu/take-away.php.