| The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA J Cubuk, JJ Alston, JJ Incicco, S Singh, MD Stuchell-Brereton, MD Ward, ... Nature communications 12 (1), 1-17, 2021 | 540 | 2021 |
| SARS-CoV-2 simulations go exascale to capture spike opening and reveal cryptic pockets across the proteome MI Zimmerman, G Bowman Biophysical Journal 120 (3), 299a, 2021 | 274* | 2021 |
| SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential N Vithani, MD Ward, MI Zimmerman, B Novak, JH Borowsky, S Singh, ... Biophysical Journal 120 (14), 2880-2889, 2021 | 80 | 2021 |
| Predicting the locations of cryptic pockets from single protein structures using the PocketMiner graph neural network A Meller, MD Ward, JH Borowsky, JM Lotthammer, M Kshirsagar, ... Nature Communications 2023 (14), 1177, 2023 | 74 | 2023 |
| Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets MD Ward, MI Zimmerman, A Meller, M Chung, SJ Swamidass, ... Nature communications 12 (1), 3023, 2021 | 61 | 2021 |
| Direct tracking of particles and quantification of margination in blood flow EJ Carboni, BH Bognet, GM Bouchillon, AL Kadilak, LM Shor, MD Ward, ... Biophysical Journal 111 (7), 1487-1495, 2016 | 47 | 2016 |
| Evaluation of the Hybrid Resolution Pace Model for the Study of Folding, Insertion and Pore Formation of Membrane Associated Peptides MD Ward, S Nangia, E May Biophysical Journal 112 (3), 525a, 2017 | 22 | 2017 |
| XenoNet: inference and likelihood of intermediate metabolite formation NR Flynn, NL Dang, MD Ward, SJ Swamidass Journal of chemical information and modeling 60 (7), 3431-3449, 2020 | 19 | 2020 |
| Deep generative design of epitope-specific binding proteins by latent conformation optimization RR Eguchi, CA Choe, U Parekh, IS Khalek, MD Ward, N Vithani, ... bioRxiv, 2022.12. 22.521698, 2022 | 9 | 2022 |
| Naturally occurring genetic variants in the oxytocin receptor alter receptor signaling profiles M Malik, MD Ward, Y Fang, JR Porter, MI Zimmerman, T Koelblen, M Roh, ... ACS Pharmacology & Translational Science 4 (5), 1543-1555, 2021 | 9 | 2021 |
| Protein sequence models for prediction and comparative analysis of the SARS-CoV-2—human interactome M Kshirsagar, N Tasnina, MD Ward, JN Law, TM Murali, JM Lavista Ferres, ... BIOCOMPUTING 2021: Proceedings of the Pacific Symposium, 154-165, 2020 | 4 | 2020 |
| Bioactivation of isoxazole-containing bromodomain and extra-terminal domain (BET) inhibitors NR Flynn, MD Ward, MA Schleiff, CMC Laurin, R Farmer, SJ Conway, ... Metabolites 11 (6), 390, 2021 | 3 | 2021 |
| Predicting cryptic pocket opening from protein structures using graph neural networks M Ward, A Meller, M Kshirsagar, F Oviedo-Perhavec, J Borowsky, G Miller, ... Machine Learning for Structural Biology Workshop, NeurIPS 2021, 2021 | | 2021 |
