Table 4.

The most native-like (three lowest RMSD) predicted loop configurations of GART, CYP119, and enolase. The ranked position of each loop configuration is shown after scoring with the DFIRE, single snapshot MM/GBSA, trajectory MM/GBSA, and the Optimized MM/GBSA-dsr scoring functions (co-crystallized ligand added).

				With co-crystallized ligand
Protein System	Backbone RMSDa	Heavy Atom RMSDa	DFIRE Rankingb	Snapshot MM/GBSAc	Traj MM/GBSAd	Optimized MM/GBSA-dsre
GART	0.57	1.15	31	5	10	40
	0.74	1.30	19	26	30	44
	1.02	1.55	45	36	23	47
CYP119	1.61	2.92	50	2	12	74
	1.79	2.76	54	8	14	39
	1.80	2.99	81	29	25	62
Enolase	1.43	1.71	81	62	66	10
	1.70	2.31	12	59	41	32
	1.75	2.96	39	29	19	12

^aRMSD in Å to known X-ray loop configuration

^bDFIRE scoring function was used to rank predicted loop configurations

^ca single minimized structure was used to calculate a MM/GBSA score and rank loop configurations

^d20 snapshots from an MD trajectory were used to calculate a MM/GBSA score and rank loop configurations

^eOptimized MM/GBSA-dsr scoring function used to score and rank loop configurations