| A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0] AT Bogetti, B Mostofian, A Dickson, AJ Pratt, AS Saglam, PO Harrison, ... Living journal of computational molecular science 1 (2), 2019 | 815 | 2019 |
| A glycan gate controls opening of the SARS-CoV-2 spike protein T Sztain, SH Ahn, AT Bogetti, L Casalino, JA Goldsmith, E Seitz, ... Nature chemistry 13 (10), 963-968, 2021 | 336 | 2021 |
| AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics L Casalino, AC Dommer, Z Gaieb, EP Barros, T Sztain, SH Ahn, A Trifan, ... The International Journal of High Performance Computing Applications 35 (5 …, 2021 | 179 | 2021 |
| # COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol A Dommer, L Casalino, F Kearns, M Rosenfeld, N Wauer, SH Ahn, ... The international journal of high performance computing applications 37 (1 …, 2023 | 80 | 2023 |
| WESTPA 2.0: High-performance upgrades for weighted ensemble simulations and analysis of longer-timescale applications JD Russo, S Zhang, JMG Leung, AT Bogetti, JP Thompson, AJ DeGrave, ... Journal of Chemical Theory and Computation 18 (2), 638-649, 2022 | 66 | 2022 |
| A minimal, adaptive binning scheme for weighted ensemble simulations PA Torrillo, AT Bogetti, LT Chong The Journal of Physical Chemistry A 125 (7), 1642-1649, 2021 | 38 | 2021 |
| A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics AT Bogetti, HE Piston, JMG Leung, CC Cabalteja, DT Yang, AJ DeGrave, ... The Journal of chemical physics 153 (6), 2020 | 25 | 2020 |
| Mechanistic Insights into Passive Membrane Permeability of Drug-like Molecules from a Weighted Ensemble of Trajectories S Zhang, JP Thompson, J Xia, AT Bogetti, F York, AG Skillman, LT Chong, ... Journal of Chemical Information and Modeling 62 (8), 1891-1904, 2022 | 22 | 2022 |
| The RED scheme: Rate-constant estimation from pre-steady state weighted ensemble simulations AJ DeGrave, AT Bogetti, LT Chong The Journal of Chemical Physics 154 (11), 2021 | 18 | 2021 |
| LPATH: A Semiautomated Python Tool for Clustering Molecular Pathways AT Bogetti, JMG Leung, LT Chong Journal of Chemical Information and Modeling 63 (24), 7610-7616, 2023 | 12 | 2023 |
| A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v0. 1] AT Bogetti, JMG Leung, JD Russo, S Zhang, JP Thompson, AS Saglam, ... bioRxiv, 2022.10. 04.510803, 2022 | 10 | 2022 |
| Direct observation of negative cooperativity in a detoxification enzyme at the atomic level by Electron Paramagnetic Resonance spectroscopy and simulation X Bogetti, A Bogetti, J Casto, G Rule, L Chong, S Saxena Protein Science 32 (10), e4770, 2023 | 9 | 2023 |
| The next frontier for designing switchable proteins: rational enhancement of kinetics AT Bogetti, MF Presti, SN Loh, LT Chong The Journal of Physical Chemistry B 125 (32), 9069-9077, 2021 | 5 | 2021 |
| Unsupervised learning of progress coordinates during weighted ensemble simulations: Application to millisecond protein folding JMG Leung, NC Frazee, A Brace, AT Bogetti, A Ramanathan, LT Chong bioRxiv, 2024.08. 28.610178, 2024 | 2 | 2024 |
| Deepdrivewe: A deep-learning-enhanced weighted ensemble rare-event sampling method NC Frazee, A Brace, A Bogetti, A Ramanathan, LT Chong Biophysical Journal 123 (3), 280a, 2024 | 2 | 2024 |
| WatFinder: a ProDy tool for protein–water interactions JM Krieger, F Doljanin, AT Bogetti, F Zhang, T Manivarma, I Bahar, ... Bioinformatics 40 (8), btae516, 2024 | 1 | 2024 |
| Revisiting textbook azide-clock reactions: A “propeller-crawling” mechanism explains differences in rates AT Bogetti, MC Zwier, LT Chong Journal of the American Chemical Society 146 (18), 12828-12835, 2024 | 1 | 2024 |
| SARS-CoV-2 glycosylated spike activation mechanism-simulations of the full unbiased pathway T Sztain-Pedone, SH Ahn, A Bogetti, L Casalino, Z Gaieb, JA McCammon, ... Biophysical Journal 120 (3), 276a, 2021 | 1 | 2021 |
| 241 A Glycan Gate Controls Opening of the SARS-CoV-2 Spike Protein T Sztain, SH Ahn, AT Bogetti, L Casalino, JA Goldsmith, E Seitz, ... Novel Developments in Cryo-EM of Biological Molecules: Resolution in Time …, 0 | 1 | |
| InSty: a ProDy module for evaluating protein interactions and stability K Mikulska-Ruminska, JM Krieger, A Banerjee, X Cao, G Wu, AT Bogetti, ... Journal of Molecular Biology, 169009, 2025 | | 2025 |