Publications

Found 1344 results
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2023
Brogan, A. P., Habib, C., Hobbs, S. J., Kranzusch, P. J., and Rudner, D. Z. (2023) Bacterial SEAL domains undergo autoproteolysis and function in regulated intramembrane proteolysis. Proc Natl Acad Sci U S A. 120, e2310862120
Li, Y., Slavik, K. M., Toyoda, H. C., Morehouse, B. R., Mann, C. C. de Olive, Elek, A., Levy, S., Wang, Z., Mears, K. S., Liu, J., Kashin, D., Guo, X., Mass, T., Sebé-Pedrós, A., Schwede, F., and Kranzusch, P. J. (2023) cGLRs are a diverse family of pattern recognition receptors in innate immunity. Cell. 186, 3261-3276.e20
Li, Y., Slavik, K. M., Toyoda, H. C., Morehouse, B. R., Mann, C. C. de Olive, Elek, A., Levy, S., Wang, Z., Mears, K. S., Liu, J., Kashin, D., Guo, X., Mass, T., Sebé-Pedrós, A., Schwede, F., and Kranzusch, P. J. (2023) cGLRs are a diverse family of pattern recognition receptors in innate immunity. Cell. 186, 3261-3276.e20
Kimani, S. W., Perveen, S., Szewezyk, M., Zeng, H., Dong, A., Li, F., Ghiabi, P., Li, Y., Chau, I., Arrowsmith, C. H., Barsyte-Lovejoy, D., Santhakumar, V., Vedadi, M., and Halabelian, L. (2023) The co-crystal structure of Cbl-b and a small-molecule inhibitor reveals the mechanism of Cbl-b inhibition. Commun Biol. 6, 1272
Passalacqua, L. F. M., Starich, M. R., Link, K. A., Wu, J., Knutson, J. R., Tjandra, N., Jaffrey, S. R., and Ferré-D'Amaré, A. R. (2023) Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture. Nat Commun. 14, 2969
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
Gao, L., Lam, K. - H., Liu, S., Przykopanski, A., Lübke, J., Qi, R., Krüger, M., Nowakowska, M. B., Selby, K., Douillard, F. P., Dorner, M. B., Perry, K., Lindström, M., Dorner, B. G., Rummel, A., and Jin, R. (2023) Crystal structures of OrfX1, OrfX2 and the OrfX1-OrfX3 complex from the orfX gene cluster of botulinum neurotoxin E1. FEBS Lett. 597, 524-537
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
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
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
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
Kwak, S. - H., C Cochrane, S., Cho, J., Dome, P. A., Ennis, A. F., Kim, J. Hyun, Zhou, P., and Hong, J. (2023) Development of LpxH inhibitors chelating the active site di-manganese metal cluster of LpxH. ChemMedChem. 10.1002/cmdc.202300023
Kwak, S. - H., C Cochrane, S., Cho, J., Dome, P. A., Ennis, A. F., Kim, J. Hyun, Zhou, P., and Hong, J. (2023) Development of LpxH inhibitors chelating the active site di-manganese metal cluster of LpxH. ChemMedChem. 10.1002/cmdc.202300023
de Miranda, R., Cuthbert, B. J., Klevorn, T., Chao, A., Mendoza, J., Arbing, M., Sieminski, P. J., Papavinasasundaram, K., Abdul-Hafiz, S., Chan, S., Sassetti, C. M., Ehrt, S., and Goulding, C. W. (2023) Differentiating the roles of Mycobacterium tuberculosis substrate binding proteins, FecB and FecB2, in iron uptake. PLoS Pathog. 19, e1011650
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
Huynh, K., Kibrom, A., Donald, B. R., and Zhou, P. (2023) Discovery, characterization, and redesign of potent antimicrobial thanatin orthologs from and targeting LptA. J Struct Biol X. 8, 100091
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
Kimani, S. W., Owen, J., Green, S. R., Li, F., Li, Y., Dong, A., Brown, P. J., Ackloo, S., Kuter, D., Yang, C., MacAskill, M., MacKinnon, S. Scott, Arrowsmith, C. H., Schapira, M., Shahani, V., and Halabelian, L. (2023) Discovery of a Novel DCAF1 Ligand Using a Drug-Target Interaction Prediction Model: Generalizing Machine Learning to New Drug Targets. J Chem Inf Model. 63, 4070-4078
Kimani, S. W., Owen, J., Green, S. R., Li, F., Li, Y., Dong, A., Brown, P. J., Ackloo, S., Kuter, D., Yang, C., MacAskill, M., MacKinnon, S. Scott, Arrowsmith, C. H., Schapira, M., Shahani, V., and Halabelian, L. (2023) Discovery of a Novel DCAF1 Ligand Using a Drug-Target Interaction Prediction Model: Generalizing Machine Learning to New Drug Targets. J Chem Inf Model. 63, 4070-4078

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