Publications

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Journal Article
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
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
Matsushita, T., Sati, G., Kondasinghe, N., Pirrone, M., Kato, T., Waduge, P., Kumar, H., Sanchon, A., Dobosz-Bartoszek, M., Shcherbakov, D., Juhas, M., Hobbie, S. N., Schrepfer, T., Chow, C. S., Polikanov, Y., Schacht, J., Vasella, A., Böttger, E. C., and Crich, D. (2019) Design, Multigram Synthesis, and in Vitro and in Vivo Evaluation of Propylamycin: A Semisynthetic 4,5-Deoxystreptamine Class Aminoglycoside for the Treatment of Drug-Resistant Enterobacteriaceae and Other Gram-Negative Pathogens. J Am Chem Soc. 10.1021/jacs.9b01693
Darabedian, N., Ji, W., Fan, M., Lin, S., Seo, H. - S., Vinogradova, E. V., Yaron, T. M., Mills, E. L., Xiao, H., Senkane, K., Huntsman, E. M., Johnson, J. L., Che, J., Cantley, L. C., Cravatt, B. F., Dhe-Paganon, S., Stegmaier, K., Zhang, T., Gray, N. S., and Chouchani, E. T. (2023) Depletion of creatine phosphagen energetics with a covalent creatine kinase inhibitor. Nat Chem Biol. 10.1038/s41589-023-01273-x
Darabedian, N., Ji, W., Fan, M., Lin, S., Seo, H. - S., Vinogradova, E. V., Yaron, T. M., Mills, E. L., Xiao, H., Senkane, K., Huntsman, E. M., Johnson, J. L., Che, J., Cantley, L. C., Cravatt, B. F., Dhe-Paganon, S., Stegmaier, K., Zhang, T., Gray, N. S., and Chouchani, E. T. (2023) Depletion of creatine phosphagen energetics with a covalent creatine kinase inhibitor. Nat Chem Biol. 10.1038/s41589-023-01273-x
Remillard, D., Buckley, D. L., Paulk, J., Brien, G. L., Sonnett, M., Seo, H. - S., Dastjerdi, S., Wühr, M., Dhe-Paganon, S., Armstrong, S. A., and Bradner, J. E. (2017) Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands. Angew Chem Int Ed Engl. 56, 5738-5743
Remillard, D., Buckley, D. L., Paulk, J., Brien, G. L., Sonnett, M., Seo, H. - S., Dastjerdi, S., Wühr, M., Dhe-Paganon, S., Armstrong, S. A., and Bradner, J. E. (2017) Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands. Angew Chem Int Ed Engl. 56, 5738-5743
Choi, M., Sukumar, N., Liu, A., and Davidson, V. L. (2009) Defining the role of the axial ligand of the type 1 copper site in amicyanin by replacement of methionine with leucine. Biochemistry. 48, 9174-84
Schureck, M. A., Dunkle, J. A., Maehigashi, T., Miles, S. J., and Dunham, C. M. (2015) Defining the mRNA recognition signature of a bacterial toxin protein. Proc Natl Acad Sci U S A. 112, 13862-7
Schureck, M. A., Dunkle, J. A., Maehigashi, T., Miles, S. J., and Dunham, C. M. (2015) Defining the mRNA recognition signature of a bacterial toxin protein. Proc Natl Acad Sci U S A. 112, 13862-7
Kohlway, A., Luo, D., Rawling, D. C., Ding, S. C., and Pyle, A. Marie (2013) Defining the functional determinants for RNA surveillance by RIG-I. EMBO Rep. 14, 772-9
Polizzi, N. F., and DeGrado, W. F. (2020) A defined structural unit enables de novo design of small-molecule-binding proteins. Science. 369, 1227-1233
Papadaki, G. F., Ani, O., Florio, T. J., Young, M. C., Danon, J. N., Sun, Y., Dersh, D., and Sgourakis, N. G. (2023) Decoupling peptide binding from T cell receptor recognition with engineered chimeric MHC-I molecules. Front Immunol. 14, 1116906
Papadaki, G. F., Ani, O., Florio, T. J., Young, M. C., Danon, J. N., Sun, Y., Dersh, D., and Sgourakis, N. G. (2023) Decoupling peptide binding from T cell receptor recognition with engineered chimeric MHC-I molecules. Front Immunol. 14, 1116906
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
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
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
Joh, N. H., Wang, T., Bhate, M. P., Acharya, R., Wu, Y., Grabe, M., Hong, M., Grigoryan, G., and DeGrado, W. F. (2014) De novo design of a transmembrane Zn²⁺-transporting four-helix bundle.. Science. 346, 1520-4
Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D., Rajashankar, K., Anderson, K. S., Baxter, R. H., Blacklow, S. C., Boggon, T. J., Bonvin, A. M. J. J., Borek, D., Brett, T. J., Caflisch, A., Chang, C. - I., Chazin, W. J., Corbett, K. D., Cosgrove, M. S., Crosson, S., Dhe-Paganon, S., Di Cera, E., Drennan, C. L., Eck, M. J., Eichman, B. F., Fan, Q. R., Ferré-D'Amaré, A. R., J Fromme, C., K Garcia, C., Gaudet, R., Gong, P., Harrison, S. C., Heldwein, E. E., Jia, Z., Keenan, R. J., Kruse, A. C., Kvansakul, M., McLellan, J. S., Modis, Y., Nam, Y., Otwinowski, Z., Pai, E. F., Pereira, P. José Barb, Petosa, C., Raman, C. S., Rapoport, T. A., Roll-Mecak, A., Rosen, M. K., Rudenko, G., Schlessinger, J., Schwartz, T. U., Shamoo, Y., Sondermann, H., Tao, Y. J., Tolia, N. H., Tsodikov, O. V., Westover, K. D., Wu, H., Foster, I., Fraser, J. S., Maia, F. R. N. C., Gonen, T., Kirchhausen, T., Diederichs, K., Crosas, M., and Sliz, P. (2016) Data publication with the structural biology data grid supports live analysis. Nat Commun. 7, 10882
Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D., Rajashankar, K., Anderson, K. S., Baxter, R. H., Blacklow, S. C., Boggon, T. J., Bonvin, A. M. J. J., Borek, D., Brett, T. J., Caflisch, A., Chang, C. - I., Chazin, W. J., Corbett, K. D., Cosgrove, M. S., Crosson, S., Dhe-Paganon, S., Di Cera, E., Drennan, C. L., Eck, M. J., Eichman, B. F., Fan, Q. R., Ferré-D'Amaré, A. R., J Fromme, C., K Garcia, C., Gaudet, R., Gong, P., Harrison, S. C., Heldwein, E. E., Jia, Z., Keenan, R. J., Kruse, A. C., Kvansakul, M., McLellan, J. S., Modis, Y., Nam, Y., Otwinowski, Z., Pai, E. F., Pereira, P. José Barb, Petosa, C., Raman, C. S., Rapoport, T. A., Roll-Mecak, A., Rosen, M. K., Rudenko, G., Schlessinger, J., Schwartz, T. U., Shamoo, Y., Sondermann, H., Tao, Y. J., Tolia, N. H., Tsodikov, O. V., Westover, K. D., Wu, H., Foster, I., Fraser, J. S., Maia, F. R. N. C., Gonen, T., Kirchhausen, T., Diederichs, K., Crosas, M., and Sliz, P. (2016) Data publication with the structural biology data grid supports live analysis. Nat Commun. 7, 10882
Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D., Rajashankar, K., Anderson, K. S., Baxter, R. H., Blacklow, S. C., Boggon, T. J., Bonvin, A. M. J. J., Borek, D., Brett, T. J., Caflisch, A., Chang, C. - I., Chazin, W. J., Corbett, K. D., Cosgrove, M. S., Crosson, S., Dhe-Paganon, S., Di Cera, E., Drennan, C. L., Eck, M. J., Eichman, B. F., Fan, Q. R., Ferré-D'Amaré, A. R., J Fromme, C., K Garcia, C., Gaudet, R., Gong, P., Harrison, S. C., Heldwein, E. E., Jia, Z., Keenan, R. J., Kruse, A. C., Kvansakul, M., McLellan, J. S., Modis, Y., Nam, Y., Otwinowski, Z., Pai, E. F., Pereira, P. José Barb, Petosa, C., Raman, C. S., Rapoport, T. A., Roll-Mecak, A., Rosen, M. K., Rudenko, G., Schlessinger, J., Schwartz, T. U., Shamoo, Y., Sondermann, H., Tao, Y. J., Tolia, N. H., Tsodikov, O. V., Westover, K. D., Wu, H., Foster, I., Fraser, J. S., Maia, F. R. N. C., Gonen, T., Kirchhausen, T., Diederichs, K., Crosas, M., and Sliz, P. (2016) Data publication with the structural biology data grid supports live analysis. Nat Commun. 7, 10882
Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D., Rajashankar, K., Anderson, K. S., Baxter, R. H., Blacklow, S. C., Boggon, T. J., Bonvin, A. M. J. J., Borek, D., Brett, T. J., Caflisch, A., Chang, C. - I., Chazin, W. J., Corbett, K. D., Cosgrove, M. S., Crosson, S., Dhe-Paganon, S., Di Cera, E., Drennan, C. L., Eck, M. J., Eichman, B. F., Fan, Q. R., Ferré-D'Amaré, A. R., J Fromme, C., K Garcia, C., Gaudet, R., Gong, P., Harrison, S. C., Heldwein, E. E., Jia, Z., Keenan, R. J., Kruse, A. C., Kvansakul, M., McLellan, J. S., Modis, Y., Nam, Y., Otwinowski, Z., Pai, E. F., Pereira, P. José Barb, Petosa, C., Raman, C. S., Rapoport, T. A., Roll-Mecak, A., Rosen, M. K., Rudenko, G., Schlessinger, J., Schwartz, T. U., Shamoo, Y., Sondermann, H., Tao, Y. J., Tolia, N. H., Tsodikov, O. V., Westover, K. D., Wu, H., Foster, I., Fraser, J. S., Maia, F. R. N. C., Gonen, T., Kirchhausen, T., Diederichs, K., Crosas, M., and Sliz, P. (2016) Data publication with the structural biology data grid supports live analysis. Nat Commun. 7, 10882
Rajashankar, K., and Dauter, Z. (2014) Data collection for crystallographic structure determination. Methods Mol Biol. 1140, 211-37
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

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