| Macromolecular modeling and design in Rosetta: recent methods and frameworks JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ... Nature methods 17 (7), 665-680, 2020 | 743 | 2020 |
| Modeling and docking of antibody structures with Rosetta BD Weitzner, JR Jeliazkov, S Lyskov, N Marze, D Kuroda, R Frick, ... Nature protocols 12 (2), 401-416, 2017 | 293 | 2017 |
| RosettaAntibodyDesign (RAbD): A general framework for computational antibody design J Adolf-Bryfogle, O Kalyuzhniy, M Kubitz, BD Weitzner, X Hu, Y Adachi, ... PLoS computational biology 14 (4), e1006112, 2018 | 216 | 2018 |
| PyIgClassify: a database of antibody CDR structural classifications J Adolf-Bryfogle, Q Xu, B North, A Lehmann, RL Dunbrack Jr Nucleic acids research 43 (D1), D432-D438, 2015 | 143 | 2015 |
| Automatically fixing errors in glycoprotein structures with Rosetta B Frenz, S Rämisch, AJ Borst, AC Walls, J Adolf-Bryfogle, WR Schief, ... Structure 27 (1), 134-139. e3, 2019 | 106 | 2019 |
| CoV3D: a database of high resolution coronavirus protein structures R Gowthaman, JD Guest, R Yin, J Adolf-Bryfogle, WR Schief, BG Pierce Nucleic acids research 49 (D1), D282-D287, 2021 | 75 | 2021 |
| Residue‐centric modeling and design of saccharide and glycoconjugate structures JW Labonte, J Adolf‐Bryfogle, WR Schief, JJ Gray Journal of computational chemistry 38 (5), 276-287, 2017 | 55 | 2017 |
| Modeling immunity with Rosetta: methods for antibody and antigen design CT Schoeder, S Schmitz, J Adolf-Bryfogle, AM Sevy, JA Finn, MF Sauer, ... Biochemistry 60 (11), 825-846, 2021 | 49 | 2021 |
| Kinase-mediated changes in nucleosome conformation trigger chromatin decondensation via poly (ADP-ribosyl) ation CJ Thomas, E Kotova, M Andrake, J Adolf-Bryfogle, R Glaser, C Regnard, ... Molecular cell 53 (5), 831-842, 2014 | 49 | 2014 |
| Better together: Elements of successful scientific software development in a distributed collaborative community J Koehler Leman, BD Weitzner, PD Renfrew, SM Lewis, R Moretti, ... PLoS computational biology 16 (5), e1007507, 2020 | 39 | 2020 |
| Hiding in plain sight: structure and sequence analysis reveals the importance of the antibody DE loop for antibody-antigen binding SP Kelow, J Adolf-Bryfogle, RL Dunbrack MAbs 12 (1), 1840005, 2020 | 31 | 2020 |
| The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite J Adolf-Bryfogle, RL Dunbrack Jr PloS one 8 (7), e66856, 2013 | 30 | 2013 |
| Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design J Adolf-Bryfogle, JW Labonte, JC Kraft, M Shapovalov, S Raemisch, ... PLoS computational biology 20 (6), e1011895, 2024 | 25 | 2024 |
| Nucleic acid delivery of immune-focused SARS-CoV-2 nanoparticles drives rapid and potent immunogenicity capable of single-dose protection KM Konrath, K Liaw, Y Wu, X Zhu, SN Walker, Z Xu, K Schultheis, ... Cell reports 38 (5), 2022 | 21 | 2022 |
| Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks J Koehler Leman, S Lyskov, SM Lewis, J Adolf-Bryfogle, RF Alford, ... Nature communications 12 (1), 6947, 2021 | 17 | 2021 |
| Development and Evaluation of GlycanDock: a protein–glycoligand docking refinement algorithm in Rosetta ML Nance, JW Labonte, J Adolf-Bryfogle, JJ Gray The Journal of Physical Chemistry B 125 (25), 6807-6820, 2021 | 17 | 2021 |
| PyRosetta Jupyter notebooks teach biomolecular structure prediction and design KH Le, J Adolf-Bryfogle, JC Klima, S Lyskov, J Labonte, S Bertolani, ... Biophysicist (Rockville, Md.) 2 (1), 108, 2021 | 16 | 2021 |
| Toward complete rational control over protein structure and function through computational design J Adolf-Bryfogle, FD Teets, CD Bahl Current opinion in structural biology 66, 170-177, 2021 | 16 | 2021 |
| Computational design of a neutralizing antibody with picomolar binding affinity for all concerning SARS-CoV-2 variants BS Jeong, JS Cha, I Hwang, U Kim, J Adolf-Bryfogle, B Coventry, HS Cho, ... MAbs 14 (1), 2021601, 2022 | 14 | 2022 |
| Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign … NE Hernandez, W Jankowski, R Frick, SP Kelow, JH Lubin, V Simhadri, ... Heliyon 9 (4), 2023 | 7 | 2023 |
