Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds von Coventry, Brian, Baker, David

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De novo design of picomolar SARS-CoV-2 miniprotein inhibitors von Cao, Longxing, Goreshnik, Inna, Coventry, Brian, Case, James Brett, Miller, Lauren, Kozodoy, Lisa, Chen, Rita E., Carter, Lauren, Walls, Alexandra C., Park, Young-Jun, Strauch, Eva-Maria, Stewart, Lance, Diamond, Michael S., Veesler, David, Baker, David

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De novo design of luciferases using deep learning von Yeh, Andy Hsien-Wei, Norn, Christoffer, Kipnis, Yakov, Tischer, Doug, Pellock, Samuel J., Evans, Declan, Ma, Pengchen, Lee, Gyu Rie, Zhang, Jason Z., Anishchenko, Ivan, Coventry, Brian, Cao, Longxing, Dauparas, Justas, Halabiya, Samer, DeWitt, Michelle, Carter, Lauren, Houk, K. N., Baker, David

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Design of protein-binding proteins from the target structure alone von Cao, Longxing, Coventry, Brian, Goreshnik, Inna, Huang, Buwei, Sheffler, William, Park, Joon Sung, Jude, Kevin M., Marković, Iva, Kadam, Rameshwar U., Verschueren, Koen H. G., Verstraete, Kenneth, Walsh, Scott Thomas Russell, Bennett, Nathaniel, Phal, Ashish, Yang, Aerin, Kozodoy, Lisa, DeWitt, Michelle, Picton, Lora, Miller, Lauren, Strauch, Eva-Maria, DeBouver, Nicholas D., Pires, Allison, Bera, Asim K., Halabiya, Samer, Hammerson, Bradley, Yang, Wei, Bernard, Steffen, Stewart, Lance, Wilson, Ian A., Ruohola-Baker, Hannele, Schlessinger, Joseph, Lee, Sangwon, Savvides, Savvas N., Garcia, K. Christopher, Baker, David

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Improving de novo protein binder design with deep learning von Bennett, Nathaniel R., Coventry, Brian, Goreshnik, Inna, Huang, Buwei, Allen, Aza, Vafeados, Dionne, Peng, Ying Po, Dauparas, Justas, Baek, Minkyung, Stewart, Lance, DiMaio, Frank, De Munck, Steven, Savvides, Savvas N., Baker, David

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De novo design of miniprotein antagonists of cytokine storm inducers von Huang, Buwei, Coventry, Brian, Borowska, Marta T., Arhontoulis, Dimitrios C., Exposit, Marc, Abedi, Mohamad, Jude, Kevin M., Halabiya, Samer F., Allen, Aza, Cordray, Cami, Goreshnik, Inna, Ahlrichs, Maggie, Chan, Sidney, Tunggal, Hillary, DeWitt, Michelle, Hyams, Nathaniel, Carter, Lauren, Stewart, Lance, Fuller, Deborah H., Mei, Ying, Garcia, K. Christopher, Baker, David

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Computational design of a neutralizing antibody with picomolar binding affinity for all concerning SARS-CoV-2 variants von Jeong, Bo-Seong, Cha, Jeong Seok, Hwang, Insu, Kim, Uijin, Adolf-Bryfogle, Jared, Coventry, Brian, Cho, Hyun-Soo, Kim, Kyun-Do, Oh, Byung-Ha

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Macromolecular modeling and design in Rosetta: recent methods and frameworks von Leman, Julia Koehler, Weitzner, Brian D., Lewis, Steven M., Adolf-Bryfogle, Jared, Alam, Nawsad, Alford, Rebecca F., Aprahamian, Melanie, Baker, David, Barlow, Kyle A., Basanta, Benjamin, Bender, Brian J., Blacklock, Kristin, Bonet, Jaume, Boyken, Scott E., Bradley, Phil, Bystroff, Chris, Conway, Patrick, Cooper, Seth, Correia, Bruno E., Coventry, Brian, Das, Rhiju, DiMaio, Frank, Dsilva, Lorna, Dunbrack, Roland, Ford, Alexander S., Fu, Darwin Y., Geniesse, Caleb, Goldschmidt, Lukasz, Gowthaman, Ragul, Gray, Jeffrey J., Gront, Dominik, Guffy, Sharon, Huang, Po-Ssu, Jacobs, Tim M., Jeliazkov, Jeliazko R., Johnson, David K., Kappel, Kalli, Karanicolas, John, Khakzad, Hamed, Khar, Karen R., Khare, Sagar D., Khatib, Firas, Khramushin, Alisa, King, Indigo C., Kleffner, Robert, Koepnick, Brian, Kortemme, Tanja, Kuenze, Georg, Kuhlman, Brian, Kuroda, Daisuke, Labonte, Jason W., Lai, Jason K., Lapidoth, Gideon, Leaver-Fay, Andrew, Lindert, Steffen, Linsky, Thomas, London, Nir, Lubin, Joseph H., Lyskov, Sergey, Maguire, Jack, Malmström, Lars, Marcos, Enrique, Marcu, Orly, Marze, Nicholas A., Meiler, Jens, Moretti, Rocco, Mulligan, Vikram Khipple, Nerli, Santrupti, Norn, Christoffer, Ollikainen, Noah, Ovchinnikov, Sergey, Pacella, Michael S., Pan, Xingjie, Park, Hahnbeom, Pavlovicz, Ryan E., Pethe, Manasi, Pilla, Kala Bharath, Raveh, Barak, Renfrew, P. Douglas, Burman, Shourya S. Roy, Rubenstein, Aliza, Sauer, Marion F., Scheck, Andreas, Schief, William, Schueler-Furman, Ora, Sedan, Yuval, Sevy, Alexander M., Sgourakis, Nikolaos G., Shi, Lei, Siegel, Justin B., Silva, Daniel-Adriano, Smith, Shannon, Song, Yifan, Stein, Amelie, Szegedy, Maria, Teets, Frank D., Thyme, Summer B., Wang, Ray Yu-Ruei, Watkins, Andrew, Zimmerman, Lior

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Perturbing the energy landscape for improved packing during computational protein design von Maguire, Jack B., Haddox, Hugh K., Strickland, Devin, Halabiya, Samer F., Coventry, Brian, Griffin, Jermel R., Pulavarti, Surya V. S. R. K, Cummins, Matthew, Thieker, David F, Klavins, Eric, Szyperski, Thomas, DiMaio, Frank, Baker, David, Kuhlman, Brian

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Randomized gates eliminate bias in sort‐seq assays von Trippe, Brian L., Huang, Buwei, DeBenedictis, Erika A., Coventry, Brian, Bhattacharya, Nicholas, Yang, Kevin K., Baker, David, Crawford, Lorin

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Accurate de novo design of heterochiral protein-protein interactions von Sun, Ke, Li, Sicong, Zheng, Bowen, Zhu, Yanlei, Wang, Tongyue, Liang, Mingfu, Yao, Yue, Zhang, Kairan, Zhang, Jizhong, Li, Hongyong, Han, Dongyang, Zheng, Jishen, Coventry, Brian, Cao, Longxing, Baker, David, Liu, Lei, Lu, Peilong

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Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins von Gerben, Stacey R, Borst, Andrew J, Hicks, Derrick R, Moczygemba, Isabelle, Feldman, David, Coventry, Brian, Yang, Wei, Bera, Asim K., Miranda, Marcos, Kang, Alex, Nguyen, Hannah, Baker, David

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Improving de novo protein binder design with deep learning von Bennett, Nathaniel R, Coventry, Brian, Goreshnik, Inna, Huang, Buwei, Allen, Aza, Vafeados, Dionne, Peng, Ying Po, Dauparas, Justas, Baek, Minkyung, Stewart, Lance, DiMaio, Frank, De Munck, Steven, Savvides, Savvas, Baker, David

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De novo design of protein homodimers containing tunable symmetric protein pockets von Hicks, Derrick R., Kennedy, Madison A., Thompson, Kirsten A., DeWitt, Michelle, Coventry, Brian, Kang, Alex, Bera, Asim K., Brunette, T. J., Sankaran, Banumathi, Stoddard, Barry, Baker, David

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Protein-binding proteins designed from target structural information von DeBouver, Nicholas, Cao, Longxing, Coventry, Brian, Bera, Asim, Yang, Wei, Bernard, Steffen, Stewart, Lance, Wilson, Ian, Ruohola-Baker, Hannele, Schlessinger, Joseph, Lee, Sangwon, Savvides, Savvas, Garcia, K. Christopher

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Blueprinting extendable nanomaterials with standardized protein blocks von Huddy, Timothy F., Hsia, Yang, Kibler, Ryan D., Xu, Jinwei, Bethel, Neville, Nagarajan, Deepesh, Redler, Rachel, Leung, Philip J. Y., Weidle, Connor, Courbet, Alexis, Yang, Erin C., Bera, Asim K., Coudray, Nicolas, Calise, S. John, Davila-Hernandez, Fatima A., Han, Hannah L., Carr, Kenneth D., Li, Zhe, McHugh, Ryan, Reggiano, Gabriella, Kang, Alex, Sankaran, Banumathi, Dickinson, Miles S., Coventry, Brian, Brunette, T. J., Liu, Yulai, Dauparas, Justas, Borst, Andrew J., Ekiert, Damian, Kollman, Justin M., Bhabha, Gira, Baker, David

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Binding and sensing diverse small molecules using shape-complementary pseudocycles von An, Linna, Said, Meerit, Tran, Long, Majumder, Sagardip, Goreshnik, Inna, Lee, Gyu Rie, Juergens, David, Dauparas, Justas, Anishchenko, Ivan, Coventry, Brian, Bera, Asim K, Kang, Alex, Levine, Paul M, Alvarez, Valentina, Pillai, Arvind, Norn, Christoffer, Feldman, David, Zorine, Dmitri, Hicks, Derrick R, Li, Xinting, Sanchez, Mariana Garcia, Vafeados, Dionne K, Salveson, Patrick J, Vorobieva, Anastassia A, Baker, David

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Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies von Edman, Natasha I., Phal, Ashish, Redler, Rachel L., Schlichthaerle, Thomas, Srivatsan, Sanjay R., Ehnes, Devon Duron, Etemadi, Ali, An, Seong J., Favor, Andrew, Li, Zhe, Praetorius, Florian, Gordon, Max, Vincent, Thomas, Marchiano, Silvia, Blakely, Leslie, Lin, Chuwei, Yang, Wei, Coventry, Brian, Hicks, Derrick R., Cao, Longxing, Bethel, Neville, Heine, Piper, Murray, Analisa, Gerben, Stacey, Carter, Lauren, Miranda, Marcos, Negahdari, Babak, Lee, Sangwon, Trapnell, Cole, Zheng, Ying, Murry, Charles E., Schweppe, Devin K., Freedman, Benjamin S., Stewart, Lance, Ekiert, Damian C., Schlessinger, Joseph, Shendure, Jay, Bhabha, Gira, Ruohola-Baker, Hannele, Baker, David

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Designed endocytosis-inducing proteins degrade targets and amplify signals von Huang, Buwei, Abedi, Mohamad, Ahn, Green, Coventry, Brian, Sappington, Isaac, Tang, Cong, Wang, Rong, Schlichthaerle, Thomas, Zhang, Jason Z, Wang, Yujia, Goreshnik, Inna, Chiu, Ching Wen, Chazin-Gray, Adam, Chan, Sidney, Gerben, Stacey, Murray, Analisa, Wang, Shunzhi, O'Neill, Jason, Yi, Li, Yeh, Ronald, Misquith, Ayesha, Wolf, Anitra, Tomasovic, Luke M, Piraner, Dan I, Duran Gonzalez, Maria J, Bennett, Nathaniel R, Venkatesh, Preetham, Ahlrichs, Maggie, Dobbins, Craig, Yang, Wei, Wang, Xinru, Sahtoe, Danny D, Vafeados, Dionne, Mout, Rubul, Shivaei, Shirin, Cao, Longxing, Carter, Lauren, Stewart, Lance, Spangler, Jamie B, Roybal, Kole T, Greisen, Per Jr, Li, Xiaochun, Bernardes, Gonçalo J L, Bertozzi, Carolyn R, Baker, David

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Design of protein-binding proteins from the target structure alone von Cao, Longxing, Coventry, Brian, Goreshnik, Inna, Huang, Buwei, Sheffler, William, Park, Joon Sung, Jude, Kevin M, Marković, Iva, Kadam, Rameshwar U, Verschueren, Koen, Verstraete, Kenneth, Walsh, Scott Thomas Russell, Bennett, Nathaniel, Phal, Ashish, Yang, Aerin, Kozodoy, Lisa, DeWitt, Michelle, Picton, Lora, Miller, Lauren, Strauch, Eva-Maria, DeBouver, Nicholas D, Pires, Allison, Bera, Asim K, Halabiya, Samer, Hammerson, Bradley, Yang, Wei, Bernard, Steffen, Stewart, Lance, Wilson, Ian A, Ruohola-Baker, Hannele, Schlessinger, Joseph, Lee, Sangwon, Savvides, Savvas, Garcia, K. Christopher, Baker, David

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