Complete combinatorial mutational enumeration of a protein functional site enables sequence‐landscape mapping and identifies highly‐mutated variants that retain activity von Colom, Mireia Solà, Vučinić, Jelena, Adolf‐Bryfogle, Jared, Bowman, James W., Verel, Sébastien, Moczygemba, Isabelle, Schiex, Thomas, Simoncini, David, Bahl, Christopher D.

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Modeling and docking of antibody structures with Rosetta von Weitzner, Brian D, Jeliazkov, Jeliazko R, Lyskov, Sergey, Marze, Nicholas, Kuroda, Daisuke, Frick, Rahel, Adolf-Bryfogle, Jared, Biswas, Naireeta, Dunbrack, Roland L, Gray, Jeffrey J

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RosettaAntibodyDesign (RAbD): A general framework for computational antibody design von Adolf-Bryfogle, Jared, Kalyuzhniy, Oleks, Kubitz, Michael, Weitzner, Brian D, Hu, Xiaozhen, Adachi, Yumiko, Schief, William R, Dunbrack, Jr, Roland L

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PyIgClassify: a database of antibody CDR structural classifications von Adolf-Bryfogle, Jared, Xu, Qifang, North, Benjamin, Lehmann, Andreas, Dunbrack, Jr, Roland L

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Residue‐centric modeling and design of saccharide and glycoconjugate structures von Labonte, Jason W., Adolf‐Bryfogle, Jared, Schief, William R., Gray, Jeffrey J.

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Development and Evaluation of GlycanDock: A Protein–Glycoligand Docking Refinement Algorithm in Rosetta von Nance, Morgan L, Labonte, Jason W, Adolf-Bryfogle, Jared, Gray, Jeffrey J

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Hiding in plain sight: structure and sequence analysis reveals the importance of the antibody DE loop for antibody-antigen binding von Kelow, Simon P., Adolf-Bryfogle, Jared, Dunbrack, Roland L.

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Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design von Adolf-Bryfogle, Jared, Labonte, Jason W, Kraft, John C, Shapovalov, Maxim, Raemisch, Sebastian, Lütteke, Thomas, DiMaio, Frank, Bahl, Christopher D, Pallesen, Jesper, King, Neil P, Gray, Jeffrey J, Kulp, Daniel W, Schief, William R

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Better together: Elements of successful scientific software development in a distributed collaborative community von Koehler Leman, Julia, Weitzner, Brian D., Renfrew, P. Douglas, Lewis, Steven M., Moretti, Rocco, Watkins, Andrew M., Mulligan, Vikram Khipple, Lyskov, Sergey, Adolf-Bryfogle, Jared, Labonte, Jason W., Krys, Justyna, Bystroff, Christopher, Schief, William, Gront, Dominik, Schueler-Furman, Ora, Baker, David, Bradley, Philip, Dunbrack, Roland, Kortemme, Tanja, Leaver-Fay, Andrew, Strauss, Charlie E. M., Meiler, Jens, Kuhlman, Brian, Gray, Jeffrey J., Bonneau, Richard

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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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The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite von Adolf-Bryfogle, Jared, Dunbrack, Jr, Roland L

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EGGNet, a Generalizable Geometric Deep Learning Framework for Protein Complex Pose Scoring von Wang, Zichen, Brand, Ryan, Adolf-Bryfogle, Jared, Grewal, Jasleen, Qi, Yanjun, Combs, Steven A., Golovach, Nataliya, Alford, Rebecca, Rangwala, Huzefa, Clark, Peter M.

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Corrigendum to “Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntib... von Hernandez, Nancy E., Jankowski, Wojciech, Frick, Rahel, Kelow, Simon P., Lubin, Joseph H., Simhadri, Vijaya, Adolf-Bryfogle, Jared, Khare, Sagar D., Dunbrack, Roland L., Gray, Jeffrey J., Sauna, Zuben E.

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Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD)... von Hernandez, Nancy E., Jankowski, Wojciech, Frick, Rahel, Kelow, Simon P., Lubin, Joseph H., Simhadri, Vijaya, Adolf-Bryfogle, Jared, Khare, Sagar D., Dunbrack, Roland L., Gray, Jeffrey J., Sauna, Zuben E.

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Biochemical and structural characterization of two cif-like epoxide hydrolases from Burkholderia cenocepacia von Taher, Noor M., Hvorecny, Kelli L., Burke, Cassandra M., Gilman, Morgan S.A., Heussler, Gary E., Adolf-Bryfogle, Jared, Bahl, Christopher D., O'Toole, George A., Madden, Dean R.

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CoV3D: a database of high resolution coronavirus protein structures von Gowthaman, Ragul, Guest, Johnathan D, Yin, Rui, Adolf-Bryfogle, Jared, Schief, William R, Pierce, Brian G

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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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Toward complete rational control over protein structure and function through computational design von Adolf-Bryfogle, Jared, Teets, Frank D, Bahl, Christopher D

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Automatically Fixing Errors in Glycoprotein Structures with Rosetta von Frenz, Brandon, Rämisch, Sebastian, Borst, Andrew J., Walls, Alexandra C., Adolf-Bryfogle, Jared, Schief, William R., Veesler, David, DiMaio, Frank

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Complete combinatorial mutational enumeration of a protein functional site enables sequence-landscape mapping and identifies highly-mutated variants that retain activity von Colom, Mireia Solà, Vučinić, Jelena, Adolf-Bryfogle, Jared, Bowman, James W, Verel, Sébastien, Moczygemba, Isabelle, Schiex, Thomas, Simoncini, David, Bahl, Christopher D

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