Table 1.

Summary and important findings of case studies in protein design field

Designed protein	Description	Main conclusion(s)	References
A retroaldol enzyme	Template-based design (using TIM-barrel template)	Designs that utilized an explicit water molecule to mediate proton shuffling were notably more favorable than those involving charged side chain networks	43
Kemp elimination enzyme	Template-based design (using TIM-barrel template) with measured rate enhancements of up to 105 and multiple turnovers	Designs were approved to have close to atomic accuracy. The results demonstrated the power of combining computational protein design with directed evolution for generating novel enzymes	70
A novel βαβ protein	De novo design included a β-sheet forming a tight core with the helix	A stand-alone βαβ motif was de novo designed with a stable tertiary structure The designed small protein may provide a model system for a protein-folding study	71
The redesign of a procarboxypeptidase	Computational protein design protocol RosettaDesign was used to completely redesign the sequence of the activation domain of human procarboxypeptidase A2	Yielding a highly stable and fast-folding antiparallel dimer	72
The design of a novel α/β protein structure, TOP7	A general computational strategy iterated between sequence design and structure prediction was used to design a 93-residue α/β protein named Top7 with a novel sequence and topology	Top7 was experimentally found to be folded and extremely stable, and the X-ray crystal structure of Top7 was similar to the design model	73