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Abstract
Proteins are increasingly used in basic and applied biomedical research. Many proteins,
however, are only marginally stable and can be expressed in limited amounts, thus
hampering research and applications. Research has revealed the thermodynamic, cellular,
and evolutionary principles and mechanisms that underlie marginal stability. With
this growing understanding, computational stability design methods have advanced over
the past two decades starting from methods that selectively addressed only some aspects
of marginal stability. Current methods are more general and, by combining phylogenetic
analysis with atomistic design, have shown drastic improvements in solubility, thermal
stability, and aggregation resistance while maintaining the protein's primary molecular
activity. Stability design is opening the way to rational engineering of improved
enzymes, therapeutics, and vaccines and to the application of protein design methodology
to large proteins and molecular activities that have proven challenging in the past.