| 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 | 729 | 2020 |
| De novo design of potent and selective mimics of IL-2 and IL-15 DA Silva, S Yu, UY Ulge, JB Spangler, KM Jude, C Labão-Almeida, LR Ali, ... Nature 565 (7738), 186-191, 2019 | 480 | 2019 |
| Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE) S Lyskov, FC Chou, SO Conchuir, BS Der, K Drew, D Kuroda, J Xu, ... PloS one 8 (5), e63906, 2013 | 452 | 2013 |
| Benchmarking and analysis of protein docking performance in Rosetta v3. 2 S Chaudhury, M Berrondo, BD Weitzner, P Muthu, H Bergman, JJ Gray PloS one 6 (8), e22477, 2011 | 350 | 2011 |
| 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 | 291 | 2017 |
| OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization G Ahdritz, N Bouatta, C Floristean, S Kadyan, Q Xia, W Gerecke, ... Nature Methods, 1-11, 2024 | 228 | 2024 |
| 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 | 207 | 2018 |
| An integrated framework advancing membrane protein modeling and design RF Alford, J Koehler Leman, BD Weitzner, AM Duran, DC Tilley, A Elazar, ... PLoS computational biology 11 (9), e1004398, 2015 | 183 | 2015 |
| Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization BD Weitzner, D Kuroda, N Marze, J Xu, JJ Gray Proteins: Structure, Function, and Bioinformatics 82 (8), 1611-1623, 2014 | 114 | 2014 |
| The origin of CDR H3 structural diversity BD Weitzner, RL Dunbrack, JJ Gray Structure 23 (2), 302-311, 2015 | 113 | 2015 |
| Real-time PyMOL visualization for Rosetta and PyRosetta EH Baugh, S Lyskov, BD Weitzner, JJ Gray PloS one 6 (8), e21931, 2011 | 92 | 2011 |
| Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites P Hosseinzadeh, PR Watson, TW Craven, X Li, S Rettie, F Pardo-Avila, ... Nature Communications 12 (1), 3384, 2021 | 62 | 2021 |
| Designing peptides on a quantum computer VK Mulligan, H Melo, HI Merritt, S Slocum, BD Weitzner, AM Watkins, ... BioRxiv, 752485, 2019 | 58 | 2019 |
| Accurate structure prediction of CDR H3 loops enabled by a novel structure-based C-terminal constraint BD Weitzner, JJ Gray The Journal of Immunology 198 (1), 505-515, 2017 | 49 | 2017 |
| A computational method for design of connected catalytic networks in proteins BD Weitzner, Y Kipnis, AG Daniel, D Hilvert, D Baker Protein Science 28 (12), 2036-2041, 2019 | 41 | 2019 |
| 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 | 37 | 2020 |
| An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases B Weitzner, T Meehan, Q Xu, RL Dunbrack Jr Proteins: Structure, Function, and Bioinformatics 75 (2), 289-295, 2009 | 24 | 2009 |
| Integration of the Rosetta suite with the python software stack via reproducible packaging and core programming interfaces for distributed simulation AS Ford, BD Weitzner, CD Bahl Protein Science 29 (1), 43-51, 2020 | 17 | 2020 |
| PyRosetta Jupyter notebooks teach biomolecular structure prediction and design KH Le, J Adolf-Bryfogle, JC Klima, S Lyskov, JW Labonte, S Bertolani, ... The Biophysicist 2 (1), 108-122, 2021 | 16 | 2021 |
| The influence of proline isomerization on potency and stability of anti-HIV antibody 10E8 M Guttman, NN Padte, Y Huang, J Yu, GJ Rocklin, BD Weitzner, M Scian, ... Scientific reports 10 (1), 14313, 2020 | 16 | 2020 |
Jeffrey J. GrayJohns Hopkins University, Chemical and Biomolecular Engineering / Program in Molecular BiophysicsVerified email at jhu.edu