GoKawiilPan, X. & Kortemme, T. Recent advances in de novo protein design: principles, methods, and applications. J. Biol. Chem. 296, 100558 (2021).
Woolfson, D. N. A brief history of de novo protein design: minimal, rational, and computational. J. Mol. Biol. 433, 167160 (2021).
Marchand, A., Van Hall-Beauvais, A. K. & Correia, B. E. Computational design of novel protein-protein interactions—an overview on methodological approaches and applications. Curr. Opin. Struct. Biol. 74, 102370 (2022).
Korendovych, I. V. & DeGrado, W. F. De novo protein design, a retrospective. Q. Rev. Biophys. 53, e3 (2020).
Khakzad, H. et al. A new age in protein design empowered by deep learning. Cell Syst. 14, 925–939 (2023).
Arnold, F. H. Directed evolution: bringing new chemistry to life. Angew. Chem. Int. Ed. 57, 4143–4148 (2018).
Zhu, J. et al. Protein assembly by design. Chem. Rev. 121, 13701–13796 (2021).
Anfinsen, C. B. Principles that govern the folding of protein chains. Science 181, 223–230 (1973). Demonstration that a protein’s amino-acid sequence intrinsically encodes its native three-dimensional structure, establishing the foundational principle for all modern protein folding and design research.
Leaver-Fay, A. et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 487, 545–574 (2011).
Kuhlman, B. et al. Design of a novel globular protein fold with atomic-level accuracy. Science 302, 1364–1368 (2003). Kuhlman et al. achieved the first atomic-level de novo design of a fully novel protein fold, providing decisive proof that computational methods can accurately encode and realize new three-dimensional protein architectures.
... continue reading