Table 1.

De novo, computationally designed proteins validated by NMR or X-ray structure determination

Year	PDB ID	Length	Fold	Experiment	Computational method
1997	1fsd	28	β−β−α motif	NMR	Pairwise residue-rotamer energy optimized by dead-end elimination (17)
1999	2a3d	73	Three-helix bundle	NMR	Started from coiled coil, hydrophobic core repacked by a genetic algorithm (9)
2003	1qys	106	Novel α+β	X-ray (1.2 Å)	Combining structure prediction with sequence design (RosettaDesign) (58)
2004	1vjq	79	α/β	X-ray (2.1 Å)	RosettaDesign (21)
2005	2cw1	65	α+β	NMR	Optimizing a knowledge-based energy score by simulated annealing (47)
2005	2a3j	127	α+β	NMR	RosettaDesign (27)
2007	2p6j	52	Three-helix bundle	NMR	Fixed binary pattern, energy optimization by dead-end elimination, side chain conformations by Monte Carlo–simulated annealing (104)
2007	3b83	100	β-sandwich	X-ray (2.4 Å)	Energy function specifically optimized for β proteins (RosettaDesign) (45)
2008	2jvf	96	α+β	NMR	Sequences generated from local tetrapeptide fragment library with some core residues fixed (108)
2009	2ki0	36	Novel β−α−β	NMR	A combination of knowledge-based secondary structure design with energy optimization (65)
2011	3u3b	113	Four-helix bundle	X-ray (1.85 Å)	Allowed backbone flexibility for redesigning the entire hydrophobic core (RosettaDesign) (81)
2011	3tdm	126	TIM-barrel α/β	X-ray (2 Å)	Imposing symmetry in RosettaDesign (36)