TABLE 3.

Detailed performance for enzyme specificity benchmark

						Find mutant amino acid starting from wild-type protein structure & mutant ligand
						CM-BR		CM-FKIC		CM-WKIC		Backrub Ensemble		Fast Design		FixBB control
Wild-type PDBID	Mutant PDBID	Wild-type Ligand	Mutant Ligand	Desired Mutation	# Design Positions	Percentile	Rank	Percentile	Rank	Percentile	Rank	Percentile	Rank	Percentile	Rank	Percentile	Rank
1A80	1M9H	NDP	NAD	K232G	5	79	22	-	100	64	37	-	100	-	100		100
1A80	1M9H	NDP	NAD	R238H	5	66	35	-	100	-	100	-	100	-	100	-	100
1FCB	1SZE	PYR	173	L230A	5	98	3	99	2	100	1	97	4	89	12	100	1
1K70	1RA0	HPY	FPY	D314A	4	100	0	98	3	99	2	100	1	98	3	99	2
1K70	1RA5	HPY	FPY	D314G	4	98	3	99	2	98	3		80		80	98	3
1K70	IRAK	HPY	FPY	D314S	4	-	80	-	80	-	80	-	80	94	6	-	80
1PK7	1OUM	ADN	TAL	M64V	3	77	15	-	60		60	-	60	-	60		60
1ZK4	1ZK1	NAP	NAD	G37D	7	99	2	98	4	100	1	99	2	100	1	100	1
2FZN	3E2Q	PRO	HYP	Y540S	2	95	3	100	1	98	2	-	40	-	40	-	40
2H6F	2H6G	FAR	GER	W602T	9	63	68	50	91	66	63	97	6	93	14	-	180
2O7B	2078	HC4	TCA	H89F	4	79	18	70	25	78	19	-	80	-	80	-	80
3HG5	3LX9	GLA	A2G	E203S	7		140		140		140	92	12		140		140
3HG5	3LX9	GLA	A2G	L206A	7	72	40	93	11		140	99	2	98	4	100	1
3KZO	3L02	ANO	SNO	E92A	5	99	2	99	2	99	2		100	100	1		100
3KZ0	3L04	ANO	SNO	E92P	5	-	100	-	100	54	47	-	100	-	100	-	100
3KZ0	3L05	ANO	SNO	E92S	5	94	7	90	11	89	12	-	100	-	100	-	100
3KZ0	3L06	ANO	SNO	E92V	5	86	15	61	40	82	19	92	9	-	100	-	100
						Find mutant amino acid starting from mutant protein structure & wild-type ligand
						CM-BR		CM-FKIC		CM-WKIC		Backrub Ensemble		Fast Design		FixBB control
Wild-type PDBID	Mutant PDBID	Wild-type Ligand	Mutant Ligand	Desired Mutation	# Design Positions	Percentile	Rank	Percentile	Rank	Percentile	Rank	Percentile	Rank	Percentile	Rank	Percentile	Rank
1A80	1M9H	NDP	NAD	K232G	5		100		100		100		100		100		100
1A80	1M9H	NDP	NAD	R238H	5		100		100		100		100		100		100
1FCB	1SZE	PYR	173	L23OA	5	97	5	96	7	96	6	88	18	-	100	-	100
1K70	1RA0	HPY	FPY	D314A	4	99	2	95	6	98	3	93	8	83	18	-	80
1K70	1RA5	HPY	FPY	D314G	4	73	23	74	22	74	22		80	-	80	-	80
1K70	IRAK	HPY	FPY	D314S	4	-	80	-	80	-	80	-	80	-	80	-	80
1PK7	1OUM	ADN	TAL	M64V	3	80	13	85	10	82	12		60	-	60		60
1ZK4	1ZK1	NAP	NAD	G37D	7	100	1	100	1	100	1	99	2		140	99	2
2FZN	3E2Q	PRO	HYP	Y54OS	2		40		40		40		40	88	22		40
2H6F	2H6G	FAR	GER	W602T	9	59	75	69	57	57	79	85	28	-	180	-	180
2O7B	2078	HC4	TCA	H89F	4	85	13	74	22		80		80		80		80
3HG5	3LX9	GLA	A2G	E203S	7	80	29	76	35	80	29	92	12	91	8	97	5
3HG5	3LX9	GLA	A2G	L206A	7	59	59	58	60	59	58		140	88	13		140
3KZ0	3L02	AN0	SN0	E92A	5	90	9	94	6	95	5	98	3	-	100	100	1
3KZ0	3L04	AN0	SN0	E92P	5	89	12	88	13	92	9	91	10	-	100	95	6
3KZ0	3L05	AN0	SN0	E92S	5	84	17	85	16	86	15	95	6	-	100	-	100
3KZ0	3L06	AN0	SN0	E92V	5	86	18	93	10	89	14	74	32	-	100	95	7

Abbreviations: CM-BR CoupledMoves with Backrub; CM-FKIC, CoupledMoves with Kinematic Closure using fragments; CM-WKIC, CoupledMoves with Kinematic Closure using “walking” perturbation.

Note: Percentile and rank are defined as in Table 2.