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De novo design of diverse small molecule binders and sensors using Shape Complementary Pseudocycles.
An L, Said M, Tran L, Majumder S, Goreshnik I, Lee GR, Juergens D, Dauparas J, Anishchenko I, Coventry B, Bera AK, Kang A, Levine PM, Alvarez V, Pillai A, Norn C, Feldman D, Zorine D, Hicks DR, Li X, Sanchez MG, Vafeados DK, Salveson PJ, Vorobieva AA, Baker D. An L, et al. Among authors: kang a. bioRxiv [Preprint]. 2023 Dec 21:2023.12.20.572602. doi: 10.1101/2023.12.20.572602. bioRxiv. 2023. PMID: 38187589 Free PMC article. Preprint.
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.
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.
Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins.
Gerben SR, Borst AJ, Hicks DR, Moczygemba I, Feldman D, Coventry B, Yang W, Bera AK, Miranda M, Kang A, Nguyen H, Baker D. Gerben SR, et al. Among authors: kang a. Biochemistry. 2023 Jan 17;62(2):358-368. doi: 10.1021/acs.biochem.2c00497. Epub 2023 Jan 10. Biochemistry. 2023. PMID: 36627259 Free PMC article.
Cyclic peptide structure prediction and design using AlphaFold.
Rettie SA, Campbell KV, Bera AK, Kang A, Kozlov S, De La Cruz J, Adebomi V, Zhou G, DiMaio F, Ovchinnikov S, Bhardwaj G. Rettie SA, et al. Among authors: kang a. bioRxiv [Preprint]. 2023 Feb 26:2023.02.25.529956. doi: 10.1101/2023.02.25.529956. bioRxiv. 2023. PMID: 36865323 Free PMC article. Preprint.
1,179 results