Publications

Found 11 results
Filters: Author is Bera, Asim K  [Clear All Filters]
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A
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
C
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
D
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
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
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
E
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
I
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
L
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