Publications

Found 22 results
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Journal Article
Li, Z., Wang, S., Nattermann, U., Bera, A. K., Borst, A. J., Yaman, M. Y., Bick, M. J., Yang, E. C., Sheffler, W., Lee, B., Seifert, S., Hura, G. L., Nguyen, H., Kang, A., Dalal, R., Lubner, J. M., Hsia, Y., Haddox, H., Courbet, A., Dowling, Q., Miranda, M., Favor, A., Etemadi, A., Edman, N. I., Yang, W., Weidle, C., Sankaran, B., Negahdari, B., Ross, M. B., Ginger, D. S., and Baker, D. (2023) Accurate computational design of three-dimensional protein crystals. Nat Mater. 10.1038/s41563-023-01683-1
Bhardwaj, G., O'Connor, J., Rettie, S., Huang, Y. - H., Ramelot, T. A., Mulligan, V. Khipple, Alpkilic, G. Gokce, Palmer, J., Bera, A. K., Bick, M. J., Di Piazza, M., Li, X., Hosseinzadeh, P., Craven, T. W., Tejero, R., Lauko, A., Choi, R., Glynn, C., Dong, L., Griffin, R., van Voorhis, W. C., Rodriguez, J., Stewart, L., Montelione, G. T., Craik, D., and Baker, D. (2022) Accurate de novo design of membrane-traversing macrocycles. Cell. 10.1016/j.cell.2022.07.019
An, L., Said, M., Tran, L., Majumder, S., Goreshnik, I., Lee, G. Rie, Juergens, D., Dauparas, J., Anishchenko, I., Coventry, B., Bera, A. K., Kang, A., Levine, P. M., Alvarez, V., Pillai, A., Norn, C., Feldman, D., Zorine, D., Hicks, D. R., Li, X., Sanchez, M. Garcia, Vafeados, D. K., Salveson, P. J., Vorobieva, A. A., and Baker, D. (2024) Binding and sensing diverse small molecules using shape-complementary pseudocycles. Science. 385, 276-282
Shi, K., Cho, S., Aukema, K. G., Lee, T., Bera, A. K., Seffernick, J. L., Wackett, L. P., and Aihara, H. (2019) Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis. PLoS One. 14, e0216979
Rettie, S. A., Campbell, K. V., Bera, A. K., Kang, A., Kozlov, S., De La Cruz, J., Adebomi, V., Zhou, G., DiMaio, F., Ovchinnikov, S., and Bhardwaj, G. (2023) Cyclic peptide structure prediction and design using AlphaFold. bioRxiv. 10.1101/2023.02.25.529956
Torres, S. Vázquez, J Y Leung, P., Venkatesh, P., Lutz, I. D., Hink, F., Huynh, H. - H., Becker, J., Yeh, A. Hsien- Wei, Juergens, D., Bennett, N. R., Hoofnagle, A. N., Huang, E., MacCoss, M. J., Expòsit, M., Lee, G. Rie, Bera, A. K., Kang, A., De La Cruz, J., Levine, P. M., Li, X., Lamb, M., Gerben, S. R., Murray, A., Heine, P., Korkmaz, E. Nihal, Nivala, J., Stewart, L., Watson, J. L., Rogers, J. M., and Baker, D. (2023) De novo design of high-affinity binders of bioactive helical peptides. Nature. 10.1038/s41586-023-06953-1
Kim, D. E., Jensen, D. R., Feldman, D., Tischer, D., Saleem, A., Chow, C. M., Li, X., Carter, L., Milles, L., Nguyen, H., Kang, A., Bera, A. K., Peterson, F. C., Volkman, B. F., Ovchinnikov, S., and Baker, D. (2023) De novo design of small beta barrel proteins. Proc Natl Acad Sci U S A. 120, e2207974120
Vorobieva, A. A., White, P., Liang, B., Horne, J. E., Bera, A. K., Chow, C. M., Gerben, S., Marx, S., Kang, A., Stiving, A. Q., Harvey, S. R., Marx, D. C., G Khan, N., Fleming, K. G., Wysocki, V. H., Brockwell, D. J., Tamm, L. K., Radford, S. E., and Baker, D. (2021) De novo design of transmembrane β barrels.. Science. 10.1126/science.abc8182
de Haas, R. J., Tas, R. P., van den Broek, D., Zheng, C., Nguyen, H., Kang, A., Bera, A. K., King, N. P., Voets, I. K., and de Vries, R. (2023) De novo designed ice-binding proteins from twist-constrained helices. Proc Natl Acad Sci U S A. 120, e2220380120
Anishchenko, I., Pellock, S. J., Chidyausiku, T. M., Ramelot, T. A., Ovchinnikov, S., Hao, J., Bafna, K., Norn, C., Kang, A., Bera, A. K., DiMaio, F., Carter, L., Chow, C. M., Montelione, G. T., and Baker, D. (2021) De novo protein design by deep network hallucination. Nature. 10.1038/s41586-021-04184-w
Sahtoe, D. D., Andrzejewska, E. A., Han, H. L., Rennella, E., Schneider, M. M., Meisl, G., Ahlrichs, M., Decarreau, J., Nguyen, H., Kang, A., Levine, P., Lamb, M., Li, X., Bera, A. K., Kay, L. E., Knowles, T. P. J., and Baker, D. (2024) Design of amyloidogenic peptide traps. Nat Chem Biol. 20, 981-990
Gerben, S. R., Borst, A. J., Hicks, D. R., Moczygemba, I., Feldman, D., Coventry, B., Yang, W., Bera, A. K., Miranda, M., Kang, A., Nguyen, H., and Baker, D. (2023) Design of Diverse Asymmetric Pockets in Homo-oligomeric Proteins. Biochemistry. 62, 358-368
Hsia, Y., Mout, R., Sheffler, W., Edman, N. I., Vulovic, I., Park, Y. - J., Redler, R. L., Bick, M. J., Bera, A. K., Courbet, A., Kang, A., Brunette, T. J., Nattermann, U., Tsai, E., Saleem, A., Chow, C. M., Ekiert, D., Bhabha, G., Veesler, D., and Baker, D. (2021) Design of multi-scale protein complexes by hierarchical building block fusion. Nat Commun. 12, 2294
Cao, L., Coventry, B., Goreshnik, I., Huang, B., Park, J. Sung, Jude, K. M., Marković, I., Kadam, R. U., Verschueren, K. H. G., Verstraete, K., Walsh, S. Thomas Rus, Bennett, N., Phal, A., Yang, A., Kozodoy, L., DeWitt, M., Picton, L., Miller, L., Strauch, E. - M., DeBouver, N. D., Pires, A., Bera, A. K., Halabiya, S., Hammerson, B., Yang, W., Bernard, S., Stewart, L., Wilson, I. A., Ruohola-Baker, H., Schlessinger, J., Lee, S., Savvides, S. N., K Garcia, C., and Baker, D. (2022) Design of protein binding proteins from target structure alone. Nature. 10.1038/s41586-022-04654-9
Davila-Hernandez, F. A., Jin, B., Pyles, H., Zhang, S., Wang, Z., Huddy, T. F., Bera, A. K., Kang, A., Chen, C. - L., De Yoreo, J. J., and Baker, D. (2023) Directing polymorph specific calcium carbonate formation with de novo protein templates. Nat Commun. 14, 8191
Moyer, A. P., Ramelot, T. A., Curti, M., Eastman, M. A., Kang, A., Bera, A. K., Tejero, R., Salveson, P. J., Curutchet, C., Romero, E., Montelione, G. T., and Baker, D. (2024) Enumerative Discovery of Noncanonical Polypeptide Secondary Structures. J Am Chem Soc. 146, 25501-25512
Said, M. Y., Kang, C. S., Wang, S., Sheffler, W., Salveson, P. J., Bera, A. K., Kang, A., Nguyen, H., Ballard, R., Li, X., Bai, H., Stewart, L., Levine, P., and Baker, D. (2022) Exploration of Structured Symmetric Cyclic Peptides as Ligands for Metal-Organic Frameworks. Chem Mater. 34, 9736-9744
An, L., Hicks, D. R., Zorine, D., Dauparas, J., Wicky, B. I. M., Milles, L. F., Courbet, A., Bera, A. K., Nguyen, H., Kang, A., Carter, L., and Baker, D. (2023) Hallucination of closed repeat proteins containing central pockets. Nat Struct Mol Biol. 30, 1755-1760
Wang, J. Yang John, Khmelinskaia, A., Sheffler, W., Miranda, M. C., Antanasijevic, A., Borst, A. J., Torres, S. V., 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, A. K., Carter, L., Fiala, B., Murphy, M., Baker, D., Ward, A. B., and King, N. P. (2023) Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proc Natl Acad Sci U S A. 120, e2214556120
Singer, J. M., Novotney, S., Strickland, D., Haddox, H. K., Leiby, N., Rocklin, G. J., Chow, C. M., Roy, A., Bera, A. K., Motta, F. C., Cao, L., Strauch, E. - M., Chidyausiku, T. M., Ford, A., Ho, E., Zaitzeff, A., Mackenzie, C. O., Eramian, H., DiMaio, F., Grigoryan, G., Vaughn, M., Stewart, L. J., Baker, D., and Klavins, E. (2022) Large-scale design and refinement of stable proteins using sequence-only models. PLoS One. 17, e0265020
Bethel, N. P., Borst, A. J., Parmeggiani, F., Bick, M. J., Brunette, T. J., Nguyen, H., Kang, A., Bera, A. K., Carter, L., Miranda, M. C., Kibler, R. D., Lamb, M., Li, X., Sankaran, B., and Baker, D. (2023) Precisely patterned nanofibres made from extendable protein multiplexes. Nat Chem. 10.1038/s41557-023-01314-x
Berger, S., Seeger, F., Yu, T. - Y., Aydin, M., Yang, H., Rosenblum, D., Guenin-Macé, L., Glassman, C., Arguinchona, L., Sniezek, C., Blackstone, A., Carter, L., Ravichandran, R., Ahlrichs, M., Murphy, M., Pultz, I. Swanson, Kang, A., Bera, A. K., Stewart, L., K Garcia, C., Naik, S., Spangler, J. B., Beigel, F., Siebeck, M., Gropp, R., and Baker, D. (2024) Preclinical proof of principle for orally delivered Th17 antagonist miniproteins. Cell. 187, 4305-4317.e18