| 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 | 559 | 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 | 411 | 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 | 394 | 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 | 328 | 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 | 262 | 2017 |
| 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 | 169 | 2015 |
| 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 | 155 | 2018 |
| 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 | 103 | 2014 |
| The origin of CDR H3 structural diversity BD Weitzner, RL Dunbrack, JJ Gray Structure 23 (2), 302-311, 2015 | 101 | 2015 |
| OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization G Ahdritz, N Bouatta, S Kadyan, Q Xia, W Gerecke, TJ O’Donnell, ... Biorxiv, 2022.11. 20.517210, 2022 | 97 | 2022 |
| Real-time PyMOL visualization for Rosetta and PyRosetta EH Baugh, S Lyskov, BD Weitzner, JJ Gray PloS one 6 (8), e21931, 2011 | 79 | 2011 |
| Designing peptides on a quantum computer VK Mulligan, H Melo, HI Merritt, S Slocum, BD Weitzner, AM Watkins, ... BioRxiv, 752485, 2019 | 52 | 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 | 45 | 2017 |
| 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 | 44 | 2021 |
| 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 | 33 | 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 | 31 | 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 | 22 | 2009 |
| A framework to simplify combined sampling strategies in Rosetta JR Porter, BD Weitzner, OF Lange PLOS one 10 (9), e0138220, 2015 | 15 | 2015 |
| 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 | 14 | 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 | 13 | 2021 |
Jeffrey J. GrayJohns Hopkins University, Chemical and Biomolecular Engineering / Program in Molecular BiophysicsVerified email at jhu.edu
