| 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 | 379 | 2020 |
| Massively parallel de novo protein design for targeted therapeutics A Chevalier, DA Silva, GJ Rocklin, DR Hicks, R Vergara, P Murapa, ... Nature 550 (7674), 74-79, 2017 | 364 | 2017 |
| Monitoring and Inhibition of Insulin Fibrillation by a Small Organic Fluorogen with Aggregation-Induced Emission Characteristics Y Hong, L Meng, S Chen, CWT Leung, L Da, M Faisal, DA Silva Manzano, ... Journal of the American Chemical Society, 2012 | 361 | 2012 |
| 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 | 331 | 2019 |
| A role for both conformational selection and induced fit in ligand binding by the LAO protein DA Silva, GR Bowman, A Sosa-Peinado, X Huang PLoS computational biology 7 (5), e1002054, 2011 | 223 | 2011 |
| De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2 TW Linsky, R Vergara, N Codina, JW Nelson, MJ Walker, W Su, ... Science 370 (6521), 1208-1214, 2020 | 159 | 2020 |
| Millisecond dynamics of RNA polymerase II translocation at atomic resolution DA Silva, DR Weiss, F Pardo Avila, LT Da, M Levitt, D Wang, X Huang Proceedings of the National Academy of Sciences 111 (21), 7665-7670, 2014 | 146 | 2014 |
| Comprehensive computational design of ordered peptide macrocycles P Hosseinzadeh, G Bhardwaj, VK Mulligan, MD Shortridge, TW Craven, ... Science 358 (6369), 1461-1466, 2017 | 143 | 2017 |
| Principles for designing proteins with cavities formed by curved β sheets E Marcos, B Basanta, TM Chidyausiku, Y Tang, G Oberdorfer, G Liu, ... Science 355 (6321), 201-206, 2017 | 125 | 2017 |
| De novo protein design by citizen scientists B Koepnick, J Flatten, T Husain, A Ford, DA Silva, MJ Bick, A Bauer, G Liu, ... Nature 570 (7761), 390-394, 2019 | 110 | 2019 |
| Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer S Berger, E Procko, D Margineantu, EF Lee, BW Shen, A Zelter, DA Silva, ... elife 5, e20352, 2016 | 85 | 2016 |
| Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue LT Da, F Pardo-Avila, L Xu, DA Silva, L Zhang, X Gao, D Wang, X Huang Nature communications 7 (1), 11244, 2016 | 81 | 2016 |
| Initiation complex structure and promoter proofreading X Liu, DA Bushnell, DA Silva, X Huang, RD Kornberg Science 333 (6042), 633-637, 2011 | 76 | 2011 |
| Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach W Zhuang, RZ Cui, DA Silva, X Huang The Journal of Physical Chemistry B, 2011 | 73 | 2011 |
| Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysis S Gu, DA Silva, L Meng, A Yue, X Huang PLoS computational biology 10 (8), e1003767, 2014 | 71 | 2014 |
| Hierarchical Nyström methods for constructing Markov state models for conformational dynamics Y Yao, RZ Cui, GR Bowman, DA Silva, J Sun, X Huang The Journal of chemical physics 138 (17), 05B602_1, 2013 | 61 | 2013 |
| Force field development for cofactors in the photosystem II L Zhang, DA Silva, YJ Yan, X Huang Journal of computational chemistry 33 (25), 1969-1980, 2012 | 59 | 2012 |
| De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures B Dang, H Wu, VK Mulligan, M Mravic, Y Wu, T Lemmin, A Ford, DA Silva, ... Proceedings of the National Academy of Sciences 114 (41), 10852-10857, 2017 | 56 | 2017 |
| Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre L Zhang, DA Silva, H Zhang, A Yue, YJ Yan, X Huang Nature Communications 5 (1), 4170, 2014 | 50 | 2014 |
| Essentials of de novo protein design: Methods and applications E Marcos, DA Silva Wiley Interdisciplinary Reviews: Computational Molecular Science, e1374, 2018 | 49 | 2018 |
Xuhui HuangHirschfelder Chair in Theoretical Chemistry, University of Wisconsin-Madison (previously at HKUST)Verified email at chem.wisc.edu
