Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides
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DOI: 10.1038/s41467-023-42434-9
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- Paulina Szymczak & Marcin Możejko & Tomasz Grzegorzek & Radosław Jurczak & Marta Bauer & Damian Neubauer & Karol Sikora & Michał Michalski & Jacek Sroka & Piotr Setny & Wojciech Kamysz & Ewa Szczurek, 2023. "Discovering highly potent antimicrobial peptides with deep generative model HydrAMP," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
- John Jumper & Richard Evans & Alexander Pritzel & Tim Green & Michael Figurnov & Olaf Ronneberger & Kathryn Tunyasuvunakool & Russ Bates & Augustin Žídek & Anna Potapenko & Alex Bridgland & Clemens Me, 2021. "Highly accurate protein structure prediction with AlphaFold," Nature, Nature, vol. 596(7873), pages 583-589, August.
- Alex Hawkins-Hooker & Florence Depardieu & Sebastien Baur & Guillaume Couairon & Arthur Chen & David Bikard, 2021. "Generating functional protein variants with variational autoencoders," PLOS Computational Biology, Public Library of Science, vol. 17(2), pages 1-23, February.
- Po-Ssu Huang & Scott E. Boyken & David Baker, 2016. "The coming of age of de novo protein design," Nature, Nature, vol. 537(7620), pages 320-327, September.
- Paulina Szymczak & Marcin Możejko & Tomasz Grzegorzek & Radosław Jurczak & Marta Bauer & Damian Neubauer & Karol Sikora & Michał Michalski & Jacek Sroka & Piotr Setny & Wojciech Kamysz & Ewa Szczurek, 2023. "Author Correction: Discovering highly potent antimicrobial peptides with deep generative model HydrAMP," Nature Communications, Nature, vol. 14(1), pages 1-1, December.
- Noelia Ferruz & Steffen Schmidt & Birte Höcker, 2022. "ProtGPT2 is a deep unsupervised language model for protein design," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
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