Table 1.

Representative examples of proteins designed using various approaches

Design principles, methodsa	Parameters introduced/optimized	Representative citations
Substitution of amino acids by rational design
Visual inspection, Docking, ISM	Substrate specificity Stereoselectivity	[1]
CAVER, ISM	Activity, Stabiliy	[3, 4]
B-Fit, ISM	Thermostability	[5]
MD-simulations	Enantioselectivity	[6, 7]
Prediction of pKa	pH Optimum	[8–11]
Computational design
FRESCO	Thermostability	[12]
CASCO Rosetta Design	Enantioselectivity	[13]
Rosetta Design/Rosetta match	Introducing new chemical activities	[14–17]
Minimalist design	Introducing new chemical activities	[18–20]
De novo design of protein folds
Semiempirical computation	Introducing catalysis	[21]
Introduction of noncanonical amino acids
Rational, substrate docking	Introducing new chemical activities	[22]
Rosetta	Protein–peptide interface, metal cofactor binding	[23, 24]
Redesign of the existing or introduction of new cofactors
Introducing metal cofactors into proteins		[25]
Substitution of metal ions in existing cofactors	Introducing new chemical activities	[26]
Transition metal complexes anchored by biotin conjugation		[27]

^aNote the list is by no means exhaustive

ISM iterative saturation mutagenesis, MD molecular dynamics, FRESCO framework for rapid enzyme stabilization by computational libraries, CASCO catalytic selectivity by computational design