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Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains.
Wang JYJ, Khmelinskaia A, Sheffler W, Miranda MC, Antanasijevic A, Borst AJ, Torres SV, Shu C, Hsia Y, Nattermann U, Ellis D, Walkey C, Ahlrichs M, Chan S, Kang A, Nguyen H, Sydeman C, Sankaran B, Wu M, Bera AK, Carter L, Fiala B, Murphy M, Baker D, Ward AB, King NP. Wang JYJ, et al. Among authors: kang a. Proc Natl Acad Sci U S A. 2023 Mar 14;120(11):e2214556120. doi: 10.1073/pnas.2214556120. Epub 2023 Mar 8. Proc Natl Acad Sci U S A. 2023. PMID: 36888664 Free PMC article.
De novo design of transmembrane β barrels.
Vorobieva AA, White P, Liang B, Horne JE, Bera AK, Chow CM, Gerben S, Marx S, Kang A, Stiving AQ, Harvey SR, Marx DC, Khan GN, Fleming KG, Wysocki VH, Brockwell DJ, Tamm LK, Radford SE, Baker D. Vorobieva AA, et al. Among authors: kang a. Science. 2021 Feb 19;371(6531):eabc8182. doi: 10.1126/science.abc8182. Science. 2021. PMID: 33602829 Free PMC article.
Design of multi-scale protein complexes by hierarchical building block fusion.
Hsia Y, Mout R, Sheffler W, Edman NI, Vulovic I, Park YJ, Redler RL, Bick MJ, Bera AK, Courbet A, Kang A, Brunette TJ, Nattermann U, Tsai E, Saleem A, Chow CM, Ekiert D, Bhabha G, Veesler D, Baker D. Hsia Y, et al. Among authors: kang a. Nat Commun. 2021 Apr 16;12(1):2294. doi: 10.1038/s41467-021-22276-z. Nat Commun. 2021. PMID: 33863889 Free PMC article.
Computational design of a synthetic PD-1 agonist.
Bryan CM, Rocklin GJ, Bick MJ, Ford A, Majri-Morrison S, Kroll AV, Miller CJ, Carter L, Goreshnik I, Kang A, DiMaio F, Tarbell KV, Baker D. Bryan CM, et al. Among authors: kang a. Proc Natl Acad Sci U S A. 2021 Jul 20;118(29):e2102164118. doi: 10.1073/pnas.2102164118. Proc Natl Acad Sci U S A. 2021. PMID: 34272285 Free PMC article.
De novo protein design by deep network hallucination.
Anishchenko I, Pellock SJ, Chidyausiku TM, Ramelot TA, Ovchinnikov S, Hao J, Bafna K, Norn C, Kang A, Bera AK, DiMaio F, Carter L, Chow CM, Montelione GT, Baker D. Anishchenko I, et al. Among authors: kang a. Nature. 2021 Dec;600(7889):547-552. doi: 10.1038/s41586-021-04184-w. Epub 2021 Dec 1. Nature. 2021. PMID: 34853475 Free PMC article.
Reconfigurable asymmetric protein assemblies through implicit negative design.
Sahtoe DD, Praetorius F, Courbet A, Hsia Y, Wicky BIM, Edman NI, Miller LM, Timmermans BJR, Decarreau J, Morris HM, Kang A, Bera AK, Baker D. Sahtoe DD, et al. Among authors: kang a. Science. 2022 Jan 21;375(6578):eabj7662. doi: 10.1126/science.abj7662. Epub 2022 Jan 21. Science. 2022. PMID: 35050655 Free PMC article.
De novo design of protein homodimers containing tunable symmetric protein pockets.
Hicks DR, Kennedy MA, Thompson KA, DeWitt M, Coventry B, Kang A, Bera AK, Brunette TJ, Sankaran B, Stoddard B, Baker D. Hicks DR, et al. Among authors: kang a. Proc Natl Acad Sci U S A. 2022 Jul 26;119(30):e2113400119. doi: 10.1073/pnas.2113400119. Epub 2022 Jul 21. Proc Natl Acad Sci U S A. 2022. PMID: 35862457 Free PMC article.
Hallucinating symmetric protein assemblies.
Wicky BIM, Milles LF, Courbet A, Ragotte RJ, Dauparas J, Kinfu E, Tipps S, Kibler RD, Baek M, DiMaio F, Li X, Carter L, Kang A, Nguyen H, Bera AK, Baker D. Wicky BIM, et al. Among authors: kang a. Science. 2022 Oct 7;378(6615):56-61. doi: 10.1126/science.add1964. Epub 2022 Sep 15. Science. 2022. PMID: 36108048 Free PMC article.
Robust deep learning-based protein sequence design using ProteinMPNN.
Dauparas J, Anishchenko I, Bennett N, Bai H, Ragotte RJ, Milles LF, Wicky BIM, Courbet A, de Haas RJ, Bethel N, Leung PJY, Huddy TF, Pellock S, Tischer D, Chan F, Koepnick B, Nguyen H, Kang A, Sankaran B, Bera AK, King NP, Baker D. Dauparas J, et al. Among authors: kang a. Science. 2022 Oct 7;378(6615):49-56. doi: 10.1126/science.add2187. Epub 2022 Sep 15. Science. 2022. PMID: 36108050 Free PMC article.
1,175 results