Publications

Found 1654 results
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2023
Harrison, S. A., Naretto, A., Balakrishnan, S., Perera, Y. R., and Chazin, W. J. (2023) Comparative analysis of the physical properties of murine and human S100A7: Insight into why zinc piracy is mediated by human but not murine S100A7. J Biol Chem. 299, 105292
Moody, J. D., Hill, S., Lundahl, M. N., Saxton, A. J., Galambas, A., Broderick, W. E., C Lawrence, M., and Broderick, J. B. (2023) Computational engineering of previously crystallized pyruvate formate-lyase activating enzyme reveals insights into SAM binding and reductive cleavage. J Biol Chem. 10.1016/j.jbc.2023.104791
Moody, J. D., Hill, S., Lundahl, M. N., Saxton, A. J., Galambas, A., Broderick, W. E., C Lawrence, M., and Broderick, J. B. (2023) Computational engineering of previously crystallized pyruvate formate-lyase activating enzyme reveals insights into SAM binding and reductive cleavage. J Biol Chem. 10.1016/j.jbc.2023.104791
Das, N. K., Hollmann, N. M., Vogt, J., Sevdalis, S. E., Banna, H. A., Ojha, M., and Koirala, D. (2023) Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element. Nat Commun. 14, 1955
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
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
Bollmeyer, M. M., Coleman, R. E., Majer, S. H., Ferrao, S. D., and Lancaster, K. M. (2023) Cytochrome P460 Cofactor Maturation Proceeds via Peroxide-Dependent Post-translational Modification. J Am Chem Soc. 145, 14404-14416
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
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
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
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
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
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
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
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
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
Sinatra, L., Vogelmann, A., Friedrich, F., Tararina, M. A., Neuwirt, E., Colcerasa, A., König, P., Toy, L., Yesiloglu, T. Z., Hilscher, S., Gaitzsch, L., Papenkordt, N., Zhai, S., Zhang, L., Romier, C., Einsle, O., Sippl, W., Schutkowski, M., Gross, O., Bendas, G., Christianson, D. W., Hansen, F. K., Jung, M., and Schiedel, M. (2023) Development of First-in-Class Dual Sirt2/HDAC6 Inhibitors as Molecular Tools for Dual Inhibition of Tubulin Deacetylation. J Med Chem. 66, 14787-14814
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
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
Harding, R. J., Franzoni, I., Mann, M. K., Szewczyk, M. M., Mirabi, B., de Freitas, R. Ferreira, Owens, D. D. G., Ackloo, S., Scheremetjew, A., Juarez-Ornelas, K. A., Sanichar, R., Baker, R. J., Dank, C., Brown, P. J., Barsyte-Lovejoy, D., Santhakumar, V., Schapira, M., Lautens, M., and Arrowsmith, C. H. (2023) Discovery and Characterization of a Chemical Probe Targeting the Zinc-Finger Ubiquitin-Binding Domain of HDAC6. J Med Chem. 66, 10273-10288
Harding, R. J., Franzoni, I., Mann, M. K., Szewczyk, M. M., Mirabi, B., de Freitas, R. Ferreira, Owens, D. D. G., Ackloo, S., Scheremetjew, A., Juarez-Ornelas, K. A., Sanichar, R., Baker, R. J., Dank, C., Brown, P. J., Barsyte-Lovejoy, D., Santhakumar, V., Schapira, M., Lautens, M., and Arrowsmith, C. H. (2023) Discovery and Characterization of a Chemical Probe Targeting the Zinc-Finger Ubiquitin-Binding Domain of HDAC6. J Med Chem. 66, 10273-10288
Harding, R. J., Franzoni, I., Mann, M. K., Szewczyk, M. M., Mirabi, B., de Freitas, R. Ferreira, Owens, D. D. G., Ackloo, S., Scheremetjew, A., Juarez-Ornelas, K. A., Sanichar, R., Baker, R. J., Dank, C., Brown, P. J., Barsyte-Lovejoy, D., Santhakumar, V., Schapira, M., Lautens, M., and Arrowsmith, C. H. (2023) Discovery and Characterization of a Chemical Probe Targeting the Zinc-Finger Ubiquitin-Binding Domain of HDAC6. J Med Chem. 66, 10273-10288
Ahmad, S., Xu, J., Feng, J. A., Hutchinson, A., Zeng, H., Ghiabi, P., Dong, A., Centrella, P. A., Clark, M. A., Guié, M. - A., Guilinger, J. P., Keefe, A. D., Zhang, Y., Cerruti, T., Cuozzo, J. W., von Rechenberg, M., Bolotokova, A., Li, Y., Loppnau, P., Seitova, A., Li, Y. - Y., Santhakumar, V., Brown, P. J., Ackloo, S., and Halabelian, L. (2023) Discovery of a First-in-Class Small-Molecule Ligand for WDR91 Using DNA-Encoded Chemical Library Selection Followed by Machine Learning. J Med Chem. 66, 16051-16061
Ahmad, S., Xu, J., Feng, J. A., Hutchinson, A., Zeng, H., Ghiabi, P., Dong, A., Centrella, P. A., Clark, M. A., Guié, M. - A., Guilinger, J. P., Keefe, A. D., Zhang, Y., Cerruti, T., Cuozzo, J. W., von Rechenberg, M., Bolotokova, A., Li, Y., Loppnau, P., Seitova, A., Li, Y. - Y., Santhakumar, V., Brown, P. J., Ackloo, S., and Halabelian, L. (2023) Discovery of a First-in-Class Small-Molecule Ligand for WDR91 Using DNA-Encoded Chemical Library Selection Followed by Machine Learning. J Med Chem. 66, 16051-16061

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