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Park, H. Ho, Logette, E., Raunser, S., Cuenin, S., Walz, T., Tschopp, J., and Wu, H. (2007) Death domain assembly mechanism revealed by crystal structure of the oligomeric PIDDosome core complex. Cell. 128, 533-46
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
Zhan, C., Patskovsky, Y., Yan, Q., Li, Z., Ramagopal, U., Cheng, H., Brenowitz, M., Hui, X., Nathenson, S. G., and Almo, S. C. (2011) Decoy strategies: the structure of TL1A:DcR3 complex. Structure. 19, 162-71
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
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
Gannam, Z. T. K., Jamali, H., Kweon, O. Sang, Herrington, J., Shillingford, S. R., Papini, C., Gentzel, E., Lolis, E., Bennett, A. M., Ellman, J. A., and Anderson, K. S. (2022) Defining the structure-activity relationship for a novel class of allosteric MKP5 inhibitors. Eur J Med Chem. 243, 114712
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
Cannon, K. A., Park, R. U., Boyken, S. E., Nattermann, U., Yi, S., Baker, D., King, N. P., and Yeates, T. O. (2019) Design and structure of two new protein cages illustrate successes and ongoing challenges in protein engineering. Protein Sci. 10.1002/pro.3802
Miller, A. Kern, Morgen, M., Steimbach, R. R., Géraldy, M., Hellweg, L., Sehr, P., Ridinger, J., Witt, O., Oehme, I., Herbst-Gervasoni, C. J., Osko, J. D., Porter, N. J., Christianson, D. W., and Gunkel, N. (2020) Design and Synthesis of Dihydroxamic Acids as HDAC6/8/10 Inhibitors. ChemMedChem. 10.1002/cmdc.202000149
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
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
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
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
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
Stille, J. K., Tjutrins, J., Wang, G., Venegas, F. A., Hennecker, C., Rueda, A. M., Sharon, I., Blaine, N., Miron, C. E., Pinus, S., Labarre, A., Plescia, J., Patrascu, M. Burai, Zhang, X., Wahba, A. S., Vlaho, D., Huot, M. J., T Schmeing, M., Mittermaier, A. K., and Moitessier, N. (2022) Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CL covalent inhibitors.. Eur J Med Chem. 229, 114046
Stille, J. K., Tjutrins, J., Wang, G., Venegas, F. A., Hennecker, C., Rueda, A. M., Sharon, I., Blaine, N., Miron, C. E., Pinus, S., Labarre, A., Plescia, J., Patrascu, M. Burai, Zhang, X., Wahba, A. S., Vlaho, D., Huot, M. J., T Schmeing, M., Mittermaier, A. K., and Moitessier, N. (2022) Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CL covalent inhibitors.. Eur J Med Chem. 229, 114046
Stille, J. K., Tjutrins, J., Wang, G., Venegas, F. A., Hennecker, C., Rueda, A. M., Sharon, I., Blaine, N., Miron, C. E., Pinus, S., Labarre, A., Plescia, J., Patrascu, M. Burai, Zhang, X., Wahba, A. S., Vlaho, D., Huot, M. J., T Schmeing, M., Mittermaier, A. K., and Moitessier, N. (2022) Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CL covalent inhibitors.. Eur J Med Chem. 229, 114046
Mandal, K., Pentelute, B. L., Bang, D., Gates, Z. P., Torbeev, V. Yu, and Kent, S. B. H. (2012) Design, total chemical synthesis, and X-ray structure of a protein having a novel linear-loop polypeptide chain topology. Angew Chem Int Ed Engl. 51, 1481-6
Soragni, A., Janzen, D. M., Johnson, L. M., Lindgren, A. G., Nguyen, A. Thai- Quynh, Tiourin, E., Soriaga, A. B., Lu, J., Jiang, L., Faull, K. F., Pellegrini, M., Memarzadeh, S., and Eisenberg, D. S. (2016) A Designed Inhibitor of p53 Aggregation Rescues p53 Tumor Suppression in Ovarian Carcinomas. Cancer Cell. 29, 90-103
Phelps, G. A., Cheramie, M. N., Fernando, D. M., Selchow, P., Meyer, C. J., Waidyarachchi, S. L., Dharuman, S., Liu, J., Meuli, M., Dal Molin, M., Killam, B. Y., Murphy, P. A., Reeve, S. M., Wilt, L. A., Anderson, S. M., Yang, L., Lee, R. B., Temrikar, Z. H., Lukka, P. B., Meibohm, B., Polikanov, Y. S., Hobbie, S. N., Böttger, E. C., Sander, P., and Lee, R. E. (2024) Development of 2nd generation aminomethyl spectinomycins that overcome native efflux in abscessus. Proc Natl Acad Sci U S A. 121, e2314101120
Phelps, G. A., Cheramie, M. N., Fernando, D. M., Selchow, P., Meyer, C. J., Waidyarachchi, S. L., Dharuman, S., Liu, J., Meuli, M., Dal Molin, M., Killam, B. Y., Murphy, P. A., Reeve, S. M., Wilt, L. A., Anderson, S. M., Yang, L., Lee, R. B., Temrikar, Z. H., Lukka, P. B., Meibohm, B., Polikanov, Y. S., Hobbie, S. N., Böttger, E. C., Sander, P., and Lee, R. E. (2024) Development of 2nd generation aminomethyl spectinomycins that overcome native efflux in abscessus. Proc Natl Acad Sci U S A. 121, e2314101120
Bloch, J. S., Mukherjee, S., Kowal, J., Filippova, E. V., Niederer, M., Pardon, E., Steyaert, J., Kossiakoff, A. A., and Locher, K. P. (2021) Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins. Proc Natl Acad Sci U S A. 10.1073/pnas.2115435118
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

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