De novo design of luciferases using deep learning

Autor: Andy Hsien-Wei Yeh, Christoffer Norn, Yakov Kipnis, Doug Tischer, Samuel J. Pellock, Declan Evans, Pengchen Ma, Gyu Rie Lee, Jason Z. Zhang, Ivan Anishchenko, Brian Coventry, Longxing Cao, Justas Dauparas, Samer Halabiya, Michelle DeWitt, Lauren Carter, K. N. Houk, David Baker

Publikováno v: Nature, vol 614, iss 7949

De novo enzyme design has sought to introduce active sites and substrate-binding pockets that are predicted to catalyse a reaction of interest into geometrically compatible native scaffolds1,2, but has been limited by a lack of suitable protein struc

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bfdc44144c91254ef60302cb67f64229
https://doi.org/10.1038/s41586-023-05696-3

Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models

Autor: Joseph L. Watson, David Juergens, Nathaniel R. Bennett, Brian L. Trippe, Jason Yim, Helen E. Eisenach, Woody Ahern, Andrew J. Borst, Robert J. Ragotte, Lukas F. Milles, Basile I. M. Wicky, Nikita Hanikel, Samuel J. Pellock, Alexis Courbet, William Sheffler, Jue Wang, Preetham Venkatesh, Isaac Sappington, Susana Vázquez Torres, Anna Lauko, Valentin De Bortoli, Emile Mathieu, Regina Barzilay, Tommi S. Jaakkola, Frank DiMaio, Minkyung Baek, David Baker

There has been considerable recent progress in designing new proteins using deep learning methods1–9. Despite this progress, a general deep learning framework for protein design that enables solution of a wide range of design challenges, includingd

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::33b3dc2111101afaf7ffd55bbbc5fd12
https://doi.org/10.1101/2022.12.09.519842

De novo protein design by deep network hallucination

Autor: David Baker, Samuel J. Pellock, Ivan Anishchenko, Tamuka M. Chidyausiku, Sergey Ovchinnikov

There has been considerable recent progress in protein structure prediction using deep neural networks to infer distance constraints from amino acid residue co-evolution1–3. We investigated whether the information captured by such networks is suffi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::5c31bf20d5e935301aa6c83bee8e504a
https://doi.org/10.1101/2020.07.22.211482

Three structurally and functionally distinct β-glucuronidases from the human gut microbe

Autor: Samuel J, Pellock, William G, Walton, Kristen A, Biernat, Dariana, Torres-Rivera, Benjamin C, Creekmore, Yongmei, Xu, Jian, Liu, Ashutosh, Tripathy, Lance J, Stewart, Matthew R, Redinbo

Publikováno v: The Journal of biological chemistry. 293(48)

The glycoside hydrolases encoded by the human gut microbiome play an integral role in processing a variety of exogenous and endogenous glycoconjugates. Here we present three structurally and functionally distinct β-glucuronidase (GUS) glycoside hydr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::98be9a6adbcf1aedc654b697a7c4d75c
https://pubmed.ncbi.nlm.nih.gov/30301767

Computational design of serine hydrolases.

Autor: Lauko A; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA.; These authors contributed equally: Anna Lauko, Samuel J. Pellock., Pellock SJ; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; These authors contributed equally: Anna Lauko, Samuel J. Pellock., Anischanka I; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Sumida KH; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Chemistry, University of Washington, Seattle, WA, USA., Juergens D; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA., Ahern W; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA., Shida A; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Hunt A; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Kalvet I; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA., Norn C; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Humphreys IR; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Jamieson C; Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA., Kang A; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Brackenbrough E; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Bera AK; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Sankaran B; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Houk KN; Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA., Baker D; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Aug 30. Date of Electronic Publication: 2024 Aug 30.