Principles for designing ideal protein structures

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Improved protein structure prediction using predicted interresidue orientations (2019, background): “From the design point of view, we have asserted previously that de novo designed proteins are “ideal” versions of naturally occurring proteins (27); the higher probability assigned by the model to designed proteins compared to naturally occurring proteins makes this assertion quantitative.”
Protein sequence design by conformational landscape optimization (2021, background): “While native structures usually require coevolution constraints derived from multiple sequence alignments to be predicted, the structures of de novo designed proteins, perhaps owing to their idealized sequence–structure encoding (9, 14), could be predicted from”
Reconfigurable asymmetric protein assemblies through implicit negative design (2021, unknown): “De novo designed protein scaffolds created by Foldit players ( 22 ) were expanded with C-terminal polyvaline helices using blueprint-based backbone generation ( 24 , 25 ).”
Recent advances in de novo protein design: Principles, methods, and applications (2021, background): “While robust protocols exist for designing helical bundles and small, idealized proteins with certain alpha-beta fold topologies (30, 58, 64), the success rates for other proteins such as beta barrels can be low (29, 31, 34).”