The PyRosetta Toolkit: A Graphical User Interface for the Rosetta Software Suite

por Adolf-Bryfogle, Jared, Dunbrack Jr., Roland L.
Publicado 2013

Hiding in plain sight: structure and sequence analysis reveals the importance of the antibody DE loop for antibody-antigen binding

por Kelow, Simon P., Adolf-Bryfogle, Jared, Dunbrack, Roland L.
Publicado 2020

PyIgClassify: a database of antibody CDR structural classifications

por Adolf-Bryfogle, Jared, Xu, Qifang, North, Benjamin, Lehmann, Andreas, Dunbrack, Roland L.
Publicado 2014

CoV3D: A database and resource for high resolution coronavirus protein structures

por Gowthaman, Ragul, Guest, Johnathan D., Yin, Rui, Adolf-Bryfogle, Jared, Schief, William R., Pierce, Brian G.
Publicado 2020

CoV3D: a database of high resolution coronavirus protein structures

por Gowthaman, Ragul, Guest, Johnathan D, Yin, Rui, Adolf-Bryfogle, Jared, Schief, William R, Pierce, Brian G
Publicado 2020

RosettaAntibodyDesign (RAbD): A general framework for computational antibody design

por Adolf-Bryfogle, Jared, Kalyuzhniy, Oleks, Kubitz, Michael, Weitzner, Brian D., Hu, Xiaozhen, Adachi, Yumiko, Schief, William R., Dunbrack, Roland L.
Publicado 2018

Automatically Fixing Errors in Glycoprotein Structures with Rosetta

por Frenz, Brandon, Rämisch, Sebastian, Borst, Andrew J., Walls, Alexandra C., Adolf-Bryfogle, Jared, Schief, William R., Veesler, David, DiMaio, Frank
Publicado 2019

Complete Combinatorial Mutational Enumeration of a protein functional site enables sequence-landscape mapping and identifies highly-mutated variants that retain activity

por Colom, Mireia Solà, Vucinic, Jelena, Adolf-Bryfogle, Jared, Bowman, James W., Verel, Sébastien, Moczygemba, Isabelle, Schiex, Thomas, Simoncini, David, Bahl, Christopher D.
Publicado 2023

Computational design of a neutralizing antibody with picomolar binding affinity for all concerning SARS-CoV-2 variants

por Jeong, Bo-Seong, Cha, Jeong Seok, Hwang, Insu, Kim, Uijin, Adolf-Bryfogle, Jared, Coventry, Brian, Cho, Hyun-Soo, Kim, Kyun-Do, Oh, Byung-Ha
Publicado 2022

Biochemical and structural characterization of two cif-like epoxide hydrolases from Burkholderia cenocepacia

por 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.
Publicado 2021

Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD)...

por 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.
Publicado 2023

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...

por 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.
Publicado 2023

Better together: Elements of successful scientific software development in a distributed collaborative community

por 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
Publicado 2020

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

por Schoeder, Clara T., Schmitz, Samuel, Adolf-Bryfogle, Jared, Sevy, Alexander M., Finn, Jessica A., Sauer, Marion F., Bozhanova, Nina G., Mueller, Benjamin K., Sangha, Amandeep K., Bonet, Jaume, Sheehan, Jonathan H., Kuenze, Georg, Marlow, Brennica, Smith, Shannon T., Woods, Hope, Bender, Brian J., Martina, Cristina E., del Alamo, Diego, Kodali, Pranav, Gulsevin, Alican, Schief, William R., Correia, Bruno E., Crowe, James E., Meiler, Jens, Moretti, Rocco
Publicado 2021

Nucleic acid delivery of immune-focused SARS-CoV-2 nanoparticles drives rapid and potent immunogenicity capable of single-dose protection

por Konrath, Kylie M., Liaw, Kevin, Wu, Yuanhan, Zhu, Xizhou, Walker, Susanne N., Xu, Ziyang, Schultheis, Katherine, Chokkalingam, Neethu, Chawla, Himanshi, Du, Jianqiu, Tursi, Nicholas J., Moore, Alan, Adolf-Bryfogle, Jared, Purwar, Mansi, Reuschel, Emma L., Frase, Drew, Sullivan, Matthew, Fry, Benjamin, Maricic, Igor, Andrade, Viviane M., Iffland, Christel, Crispin, Max, Broderick, Kate E., Humeau, Laurent M.P.F., Patel, Ami, Smith, Trevor R.F., Pallesen, Jesper, Weiner, David B., Kulp, Daniel W.
Publicado 2022

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

por Koehler Leman, Julia, Lyskov, Sergey, Lewis, Steven M., Adolf-Bryfogle, Jared, Alford, Rebecca F., Barlow, Kyle, Ben-Aharon, Ziv, Farrell, Daniel, Fell, Jason, Hansen, William A., Harmalkar, Ameya, Jeliazkov, Jeliazko, Kuenze, Georg, Krys, Justyna D., Ljubetič, Ajasja, Loshbaugh, Amanda L., Maguire, Jack, Moretti, Rocco, Mulligan, Vikram Khipple, Nance, Morgan L., Nguyen, Phuong T., Ó Conchúir, Shane, Roy Burman, Shourya S., Samanta, Rituparna, Smith, Shannon T., Teets, Frank, Tiemann, Johanna K. S., Watkins, Andrew, Woods, Hope, Yachnin, Brahm J., Bahl, Christopher D., Bailey-Kellogg, Chris, Baker, David, Das, Rhiju, DiMaio, Frank, Khare, Sagar D., Kortemme, Tanja, Labonte, Jason W., Lindorff-Larsen, Kresten, Meiler, Jens, Schief, William, Schueler-Furman, Ora, Siegel, Justin B., Stein, Amelie, Yarov-Yarovoy, Vladimir, Kuhlman, Brian, Leaver-Fay, Andrew, Gront, Dominik, Gray, Jeffrey J., Bonneau, Richard
Publicado 2021