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Protein interactions in human pathogens revealed through deep learning.
Humphreys IR, Zhang J, Baek M, Wang Y, Krishnakumar A, Pei J, Anishchenko I, Tower CA, Jackson BA, Warrier T, Hung DT, Peterson SB, Mougous JD, Cong Q, Baker D. Humphreys IR, et al. Nat Microbiol. 2024 Oct;9(10):2642-2652. doi: 10.1038/s41564-024-01791-x. Epub 2024 Sep 18. Nat Microbiol. 2024. PMID: 39294458 Free PMC article.
Computed structures of core eukaryotic protein complexes.
Humphreys IR, Pei J, Baek M, Krishnakumar A, Anishchenko I, Ovchinnikov S, Zhang J, Ness TJ, Banjade S, Bagde SR, Stancheva VG, Li XH, Liu K, Zheng Z, Barrero DJ, Roy U, Kuper J, Fernández IS, Szakal B, Branzei D, Rizo J, Kisker C, Greene EC, Biggins S, Keeney S, Miller EA, Fromme JC, Hendrickson TL, Cong Q, Baker D. Humphreys IR, et al. Science. 2021 Dec 10;374(6573):eabm4805. doi: 10.1126/science.abm4805. Epub 2021 Dec 10. Science. 2021. PMID: 34762488 Free PMC article.
Essential and virulence-related protein interactions of pathogens revealed through deep learning.
Humphreys IR, Zhang J, Baek M, Wang Y, Krishnakumar A, Pei J, Anishchenko I, Tower CA, Jackson BA, Warrier T, Hung DT, Peterson SB, Mougous JD, Cong Q, Baker D. Humphreys IR, et al. bioRxiv [Preprint]. 2024 Apr 12:2024.04.12.589144. doi: 10.1101/2024.04.12.589144. bioRxiv. 2024. Update in: Nat Microbiol. 2024 Oct;9(10):2642-2652. doi: 10.1038/s41564-024-01791-x. PMID: 38645026 Free PMC article. Updated. Preprint.
Genetic manipulation of candidate phyla radiation bacteria provides functional insights into microbial dark matter.
Wang Y, Gallagher LA, Andrade PA, Liu A, Humphreys IR, Turkarslan S, Cutler KJ, Arrieta-Ortiz ML, Li Y, Radey MC, McLean JS, Cong Q, Baker D, Baliga NS, Peterson SB, Mougous JD. Wang Y, et al. Among authors: humphreys ir. bioRxiv [Preprint]. 2023 May 11:2023.05.02.539146. doi: 10.1101/2023.05.02.539146. bioRxiv. 2023. Update in: Cell. 2023 Oct 26;186(22):4803-4817.e13. doi: 10.1016/j.cell.2023.08.017. PMID: 37205512 Free PMC article. Updated. Preprint.
Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle.
Wang Y, Gallagher LA, Andrade PA, Liu A, Humphreys IR, Turkarslan S, Cutler KJ, Arrieta-Ortiz ML, Li Y, Radey MC, McLean JS, Cong Q, Baker D, Baliga NS, Peterson SB, Mougous JD. Wang Y, et al. Among authors: humphreys ir. Cell. 2023 Oct 26;186(22):4803-4817.e13. doi: 10.1016/j.cell.2023.08.017. Epub 2023 Sep 7. Cell. 2023. PMID: 37683634 Free PMC article.
Generalized biomolecular modeling and design with RoseTTAFold All-Atom.
Krishna R, Wang J, Ahern W, Sturmfels P, Venkatesh P, Kalvet I, Lee GR, Morey-Burrows FS, Anishchenko I, Humphreys IR, McHugh R, Vafeados D, Li X, Sutherland GA, Hitchcock A, Hunter CN, Kang A, Brackenbrough E, Bera AK, Baek M, DiMaio F, Baker D. Krishna R, et al. Among authors: humphreys ir. Science. 2024 Apr 19;384(6693):eadl2528. doi: 10.1126/science.adl2528. Epub 2024 Apr 19. Science. 2024. PMID: 38452047 Free article.
Rapid and accurate prediction of protein homo-oligomer symmetry with Seq2Symm.
Kshirsagar M, Meller A, Humphreys I, Sledzieski S, Xu Y, Dodhia R, Horvitz E, Berger B, Bowman G, Ferres JL, Baker D, Baek M. Kshirsagar M, et al. Res Sq [Preprint]. 2024 Apr 26:rs.3.rs-4215086. doi: 10.21203/rs.3.rs-4215086/v1. Res Sq. 2024. PMID: 38746169 Free PMC article. Preprint.
83 results