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Nayak, D., Lv, D., Yuan, Y., Zhang, P., Hu, W., Nayak, A., Ruben, E. A., Lv, Z., Sung, P., Hromas, R., Zheng, G., Zhou, D., and Olsen, S. K. (2024) Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL. Nat Commun. 15, 2743
Mahoney, B. J., Goring, A. K., Wang, Y., Dasika, P., Zhou, A., Grossbard, E., Cascio, D., Loo, J. A., and Clubb, R. T. (2023) Development and atomic structure of a new fluorescence-based sensor to probe heme transfer in bacterial pathogens. J Inorg Biochem. 249, 112368
Berk, J. M., Lim, C., Ronau, J. A., Chaudhuri, A., Chen, H., Beckmann, J. F., J Loria, P., Xiong, Y., and Hochstrasser, M. (2020) A deubiquitylase with an unusually high-affinity ubiquitin-binding domain from the scrub typhus pathogen Orientia tsutsugamushi. Nat Commun. 11, 2343
Saotome, K., Singh, A. K., and Sobolevsky, A. I. (2018) Determining the Crystal Structure of TRPV6. in Calcium Entry Channels in Non-Excitable Cells, pp. 275-292, Calcium Entry Channels in Non-Excitable Cells, Boca Raton (FL), 10.1201/9781315152592-14
Banigan, J. R., Mandal, K., Sawaya, M. R., Thammavongsa, V., Hendrickx, A. P. A., Schneewind, O., Yeates, T. O., and Kent, S. B. H. (2010) Determination of the X-ray structure of the snake venom protein omwaprin by total chemical synthesis and racemic protein crystallography. Protein Sci. 19, 1840-9
Gareau, J. R., Reverter, D., and Lima, C. D. (2012) Determinants of small ubiquitin-like modifier 1 (SUMO1) protein specificity, E3 ligase, and SUMO-RanGAP1 binding activities of nucleoporin RanBP2. J Biol Chem. 287, 4740-51
Dutta, S., Gullá, S., T Chen, S., Fire, E., Grant, R. A., and Keating, A. E. (2010) Determinants of BH3 binding specificity for Mcl-1 versus Bcl-xL. J Mol Biol. 398, 747-62
Witkowski, W. A., and Hardy, J. A. (2011) A designed redox-controlled caspase. Protein Sci. 20, 1421-31
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
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
Dziedzic, P., Cisneros, J. A., Robertson, M. J., Hare, A. A., Danford, N. E., Baxter, R. H. G., and Jorgensen, W. L. (2015) Design, synthesis, and protein crystallography of biaryltriazoles as potent tautomerase inhibitors of macrophage migration inhibitory factor. J Am Chem Soc. 137, 2996-3003
Tago, N., Katolik, A., Clark, N. E., Montemayor, E. J., Seio, K., Sekine, M., P Hart, J., and Damha, M. J. (2015) Design, Synthesis, and Properties of Phosphoramidate 2',5'-Linked Branched RNA: Toward the Rational Design of Inhibitors of the RNA Lariat Debranching Enzyme. J Org Chem. 80, 10108-18
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
Decroos, C., and Christianson, D. W. (2015) Design, Synthesis, and Evaluation of Polyamine Deacetylase Inhibitors, and High-Resolution Crystal Structures of Their Complexes with Acetylpolyamine Amidohydrolase. Biochemistry. 54, 4692-703
Rugel, A., Tarpley, R. S., Lopez, A., Menard, T., Guzman, M. A., Taylor, A. B., Cao, X., Kovalskyy, D., Chevalier, F. D., Anderson, T. J. C., P Hart, J., LoVerde, P. T., and McHardy, S. F. (2018) Design, Synthesis, and Characterization of Novel Small Molecules as Broad Range Antischistosomal Agents. ACS Med Chem Lett. 9, 967-973
Carter, Z. J., Hollander, K., Spasov, K. A., Anderson, K. S., and Jorgensen, W. L. (2023) Design, synthesis, and biological testing of biphenylmethyloxazole inhibitors targeting HIV-1 reverse transcriptase. Bioorg Med Chem Lett. 84, 129216
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
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
Maniaci, B., Lipper, C. H., Anipindi, D. L., Erlandsen, H., Cole, J. L., Stec, B., Huxford, T., and Love, J. J. (2019) Design of High-Affinity Metal-Controlled Protein Dimers. Biochemistry. 58, 2199-2207
Broerman, A. J., Pollmann, C., Zhao, Y., Lichtenstein, M. A., Jackson, M. D., Tessmer, M. H., Ryu, W. Hee, Ogishi, M., Abedi, M. H., Sahtoe, D. D., Allen, A., Kang, A., De La Cruz, J., Brackenbrough, E., Sankaran, B., Bera, A. K., Zuckerman, D. M., Stoll, S., K Garcia, C., Praetorius, F., Piehler, J., and Baker, D. (2025) Design of facilitated dissociation enables timing of cytokine signalling. Nature. 10.1038/s41586-025-09549-z
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
Wright, N. J., Matsuoka, Y., Park, H., He, W., Webster, C. G., Furutani, K., Fedor, J. G., McGinnis, A., Zhao, Y., Chen, O., Bang, S., Fan, P., Spasojevic, I., Hong, J., Ji, R. - R., and Lee, S. - Y. (2024) Design of an equilibrative nucleoside transporter subtype 1 inhibitor for pain relief. Nat Commun. 15, 10738
Sahtoe, D. D., Andrzejewska, E. A., Han, H. L., Rennella, E., Schneider, M. M., Meisl, G., Ahlrichs, M., Decarreau, J., Nguyen, H., Kang, A., Levine, P., Lamb, M., Li, X., Bera, A. K., Kay, L. E., Knowles, T. P. J., and Baker, D. (2024) Design of amyloidogenic peptide traps. Nat Chem Biol. 20, 981-990
Wittlinger, F., Heppner, D. E., To, C., Günther, M., Shin, B. Hee, Rana, J. K., Schmoker, A. M., Beyett, T. S., Berger, L. M., Berger, B. - T., Bauer, N., Vasta, J. D., Corona, C. R., Robers, M. B., Knapp, S., Jänne, P. A., Eck, M. J., and Laufer, S. A. (2021) Design of a "Two-in-One" Mutant-Selective Epidermal Growth Factor Receptor Inhibitor That Spans the Orthosteric and Allosteric Sites. J Med Chem. 10.1021/acs.jmedchem.1c00848
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

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