From DNA sequence to improved functionality: using protein sequence comparisons to rapidly design a thermostable consensus phytase.

By M. Lehmann, D. Kostrewa, M. Wyss, R. Brugger, A. D'arcy, L. Pasamontes, A. M. V. Loon. 2000

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Generating functional protein variants with variational autoencoders (2020, background): “Indeed, evolutionary information from alignments has previously proven useful in protein design and engineering [33–35].”
The ankyrin repeat as molecular architecture for protein recognition (2004, methodology): “Alignment of 13 fungal phytase sequences was used to create a consensus phytase with normal enzymatic activity but significantly higher thermostability (Lehmann et al. 2000).”
Consensus protein design (2016, background): “…stability, with ∼10% being stability neutral and ∼40% being destabilising, leading to challenges and trade-offs during implementation (Steipe et al., 1994; Nikolova et al., 1998; Wang et al., 1999; Lehmann et al., 2000, 2002; Lehmann and Wyss, 2001; Polizzi et al., 2006; Khersonsky et al., 2012).”
Design of novel FN3 domains with high stability by a consensus sequence approach. (2012, methodology): “…2006; Gribenko et al., 2009), directed evolution (Giver et al., 1998; Miyazaki et al., 2000; Miyazaki et al., 2006; Kotzia and Labrou, 2009), composition of consensus sequences (Lehmann et al., 2000a,b), design of stabilizing salt bridges or disulfides and other methods (Lehmann and Wyss, 2001).”