Table 4.

Catalytic site and DNA binding predictions for R1057 and R1068 targets, comparing results for the crystal structure, the refinement target and selected refined versions thereof. Included are the five models of the top four groups along with model_1 from the other six groups that were ranked in the top 10 for both targets. CatsID identifies structural matches to catalytic sites among all Protein Data Bank proteins; scores listed are for methyltransferase hits. Scores above 0.02 are an indication of correct assignment of catalytic function. No models surpassed this threshold for a methyltransferase hit, but scores for any methyltransferase hits are displayed (bold). It should be noted also that where a methyltransferase hit was recorded, other hits with unrelated catalytic sites also were observed. For ProFunc scores, the higher the score of an active site template match the greater the confidence in a hit: methyltransferase hit scores are again highlighted in bold. DNAbind predicts DNA-binding ability even from low-resolution, Cα-only protein models: proteins with scores above the 0.5313 threshold are predicted to bind DNA (bold). BindUP predicts nucleic acid binding function given the protein’s three-dimensional structure.

					R1057		R1068
		GDT_HA	CatsID	ProFunc	DNAbind	BindUP	GDT_HA	DNAbind	BindUP
Crystal		-	0.004	82.04	0.663	YES	-	0.991	YES
Refinement target		44.11	No hits	81.14	0.476	NO	21.612	0.959	YES
FEIG-S refinements	model_1	75.10	No hits	0	0.535	NO	43.58	0.989	YES
	model_2	70.20	No hits	0	0.497	NO	38.13	0.989	YES
	model_3	74.60	No hits	0	0.531	NO	38.41	0.989	YES
	model_4	72.20	No hits	0	0.535	NO	40.36	0.991	YES
	model_5	74.00	No hits	80.5	0.527	NO	42.60	0.990	YES
DellaCorteLab refinements	model_1	64.40	No hits	83.0	0.515	NO	43.30	0.989	YES
	model_2	66.40	No hits	0	0.509	NO	42.60	0.989	YES
	model_3	66.10	No hits	87.0	0.529	NO	42.32	0.990	YES
	model_4	66.10	No hits	83.0	0.506	NO	42.64	0.989	YES
	model_5	66.20	No hits	81.1	0.547	NO	40.64	0.989	YES
FEIG refinements	model_1	71.60	0.005	0	0.068	NO	46.23	0.987	YES
	model_2	70.90	No hits	90.1	0.525	NO	44.55	0.989	YES
	model_3	67.90	No hits	0	0.065	NO	44.13	0.990	YES
	model_4	67.40	0.004	0	0.496	NO	43.85	0.988	YES
	model_5	67.80	0.005	0	0.483	NO	36.87	0.986	YES
Baker refinements	model_1	70.90	No hits	83.0	0.511	NO	40.64	0.986	YES
	model_2	67.80	0.004	83.0	0.491	NO	40.92	0.985	YES
	model_3	64.40	0.004	124.0	0.469	NO	32.82	0.978	YES
	model_4	65.30	0.004	0	0.457	NO	32.26	0.986	YES
	model_5	62.20	No hits	81.1	0.547	NO	32.68	0.989	YES