Table 2.

Top 20 threading models ranked by constraint error

Name	Fold family	% Sequence identity	Threading rank	Constraint error, Å*	Number of violations†
FGF-2	β-Trefoil	98.6	1	0.0	0
IL-1β	β-Trefoil	12.7	5	0.0	0
Gastrotropin	Lipocalin	7.1	8	2.9	1
Hisactophilin	β-Trefoil	8.6	12	5.5	2
Guanylate kinase	P-loop	12.4	9	7.4	4
NTP pyrophosphohydrolase	NTP pyrophosphohydrolase	9.3	6	14.5	3
Glutathione peroxidase	Thioredoxin	11.1	14	16.6	5
Retinol-binding protein	Lipocalin	9.1	18	17.1	3
Nucleoside diphosphokinase	Ferridoxin-like	8.8	20	18.6	2
Cytochrome c4	Cytochrome c	12.6	11	21.4	5
Aspartate carbamoyltransferase	Ferridoxin-like	9.8	13	22.6	4
D-UTPase	β-Clip	7.8	2	27.5	7
Disulfide bond formation protein	Thioredoxin	8.4	15	28.1	8
ASV integrase	Ribonuclease H-like	7.8	19	28.6	5
Endoglucanase C	Galactose binding	11.6	4	33.8	6
TATA-box-binding protein	TATA-box-binding protein-like	10.3	7	40.0	8
Phospholipase A2	Phospholipase A2	9.5	16	55.4	7
PRD paired domain	3-Helix bundle	12.7	17	143.4	8

Two models, 2PLDA (3) and 2PHY (10), had <50% of the distance constraints defined and were subsequently removed from the analysis. Undefined constraints resulted from lysines paired to gaps or unresolved regions in the model structure. 

^*Constraint error is the extent of model violation of the cross-link-derived distance constraints, as defined by Eq. 1. 

^† Number of violations is the number of experimentally derived constraints violated by the model (i.e., the number of cross-linked Lys-Lys C^α distances > 24 Å).