TABLE 1.
Summary of the key deep learning protein design methods discussed in this review, with their generation type and generative model type indicated by a *. ∼ in the structure design field suggests that some minor design coincides with sequence design. The design target of each method is also provided.
| Method | Generation type | Generative model | Design target | |||
|---|---|---|---|---|---|---|
| Sequence | Structure | VAE | GAN | Autoregressive | ||
| Grisoni et al. (2018) | * | * | Antimicrobial peptides | |||
| Müller et al. (2018) | * | * | Membranolytic anticancer peptides | |||
| PepCVAE | * | * | Antimicrobial peptides | |||
| Hawkins-Hooker et al. (2021) | * | * | Luciferase enzymes | |||
| ProteinGAN | * | * | MDH-like enzymes | |||
| Greener et al. (2018) | * | * | Metalloproteins | |||
| Gupta and Zou (2019) | * | * | Antimicrobial peptides | |||
| Amimeur et al. (2020) | * | * | Human antibodies | |||
| Ingraham et al. (2019) | * | * | Non-specific | |||
| ProteoGAN | * | * | Non-specific | |||
| ProteinSolver | * | * | Non-specific | |||
| Anand et al. (2022) | * | * | Non-specific | |||
| Ig-VAE | * | * | Immunoglobulins | |||
| Anand et al. (2019) | * | * | Non-specific | |||
| Tischer et al. (2020) | * | ∼ | Inverted structure prediction model | Non-specific | ||
| Anishchenko et al. (2021) | * | * | Inverted structure prediction model | Non-specific | ||
| Norn et al. (2021) | * | ∼ | Inverted structure prediction model | Non-specific | ||