Table 3.

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.

			Without co-crystallized ligand
Protein System	Backbone RMSDa	Heavy Atom RMSDa	DFIREb	Snapshot MM/GBSAc	Traj MM/GBSAd	Optimized MM/GBSA-dsre
GART	0.57	1.15	31	3	9	87
	0.74	1.30	19	46	74	68
	1.02	1.55	45	91	69	18
CYP119	1.61	2.92	50	6	37	87
	1.79	2.76	54	9	10	64
	1.80	2.99	81	50	87	96
Enolase	1.43	1.71	81	6	18	97
	1.70	2.31	12	9	38	83
	1.75	2.96	39	25	77	29

^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