| Simulation-based approaches for determining membrane permeability of small compounds CT Lee, J Comer, C Herndon, N Leung, A Pavlova, RV Swift, C Tung, ... Journal of chemical information and modeling 56 (4), 721-733, 2016 | 223 | 2016 |
| Supercomputer-based ensemble docking drug discovery pipeline with application to COVID-19 A Acharya, R Agarwal, MB Baker, J Baudry, D Bhowmik, S Boehm, ... Journal of chemical information and modeling 60 (12), 5832-5852, 2020 | 176 | 2020 |
| Accelerating membrane simulations with hydrogen mass repartitioning C Balusek, H Hwang, CH Lau, K Lundquist, A Hazel, A Pavlova, DL Lynch, ... Journal of chemical theory and computation 15 (8), 4673-4686, 2019 | 128 | 2019 |
| Accurate determination of protein: ligand standard binding free energies from molecular dynamics simulations H Fu, H Chen, M Blazhynska, E Goulard Coderc de Lacam, ... Nature protocols 17 (4), 1114-1141, 2022 | 86 | 2022 |
| Understanding the Role of Water in Aqueous Ruthenium‐Catalyzed Transfer Hydrogenation of Ketones. A Pavlova, EJ Meijer ChemPhysChem 13 (15), 3492-3496, 2012 | 84 | 2012 |
| Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease A Pavlova, DL Lynch, I Daidone, L Zanetti-Polzi, MD Smith, C Chipot, ... Chemical science 12 (4), 1513-1527, 2021 | 62 | 2021 |
| Machine learning reveals the critical interactions for SARS-CoV-2 spike protein binding to ACE2 A Pavlova, Z Zhang, A Acharya, DL Lynch, YT Pang, Z Mou, JM Parks, ... The journal of physical chemistry letters 12 (23), 5494-5502, 2021 | 55 | 2021 |
| SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact YT Pang, A Acharya, DL Lynch, A Pavlova, JC Gumbart Communications Biology 5 (1), 1170, 2022 | 53 | 2022 |
| Living on the edge: simulations of bacterial outer-membrane proteins A Pavlova, H Hwang, K Lundquist, C Balusek, JC Gumbart Biochimica et Biophysica Acta (BBA)-Biomembranes 1858 (7), 1753-1759, 2016 | 45 | 2016 |
| Clarifying the role of sodium in the silica oligomerization reaction A Pavlova, TT Trinh, RA van Santen, EJ Meijer Physical Chemistry Chemical Physics 15 (4), 1123-1129, 2013 | 38 | 2013 |
| Tuning proton transfer thermodynamics in SARS-CoV-2 main protease: implications for catalysis and inhibitor design L Zanetti-Polzi, MD Smith, C Chipot, JC Gumbart, DL Lynch, A Pavlova, ... The journal of physical chemistry letters 12 (17), 4195-4202, 2021 | 29 | 2021 |
| Development of CHARMM-compatible force-field parameters for cobalamin and related cofactors from quantum mechanical calculations A Pavlova, JM Parks, JC Gumbart Journal of chemical theory and computation 14 (2), 784-798, 2018 | 29 | 2018 |
| ACE2 glycans preferentially interact with SARS-CoV-2 over SARS-CoV A Acharya, DL Lynch, A Pavlova, YT Pang, JC Gumbart Chemical Communications 57 (48), 5949-5952, 2021 | 24 | 2021 |
| Understanding virus structure and dynamics through molecular simulations DL Lynch, A Pavlova, Z Fan, JC Gumbart Journal of Chemical Theory and Computation 19 (11), 3025-3036, 2023 | 22 | 2023 |
| Mechanistic aspects of using formate as a hydrogen donor in aqueous transfer hydrogenation A Pavlova, E Rosler, EJ Meijer ACS Catalysis 6 (8), 5350-5358, 2016 | 22 | 2016 |
| Parametrization of macrolide antibiotics using the force field toolkit A Pavlova, JC Gumbart Journal of computational chemistry 36 (27), 2052-2063, 2015 | 21 | 2015 |
| Synergistic biophysical techniques reveal structural mechanisms of engineered cationic antimicrobial peptides in lipid model membranes F Heinrich, A Salyapongse, A Kumagai, FG Dupuy, K Shukla, A Penk, ... Chemistry–A European Journal 26 (28), 6247-6256, 2020 | 19 | 2020 |
| Restoring and enhancing the potency of existing antibiotics against drug-resistant gram-negative bacteria through the development of potent small-molecule adjuvants B Yu, M Roy Choudhury, X Yang, SL Benoit, E Womack, ... ACS Infectious Diseases 8 (8), 1491-1508, 2022 | 18 | 2022 |
| The mechanism of action of hepatitis B virus capsid assembly modulators can be predicted from binding to early assembly intermediates A Pavlova, L Bassit, BD Cox, M Korablyov, C Chipot, D Patel, DL Lynch, ... Journal of medicinal chemistry 65 (6), 4854-4864, 2022 | 18 | 2022 |
| Redox-driven conformational dynamics in a photosystem-II-inspired β-hairpin maquette determined through spectroscopy and simulation H Hwang, TG McCaslin, A Hazel, CV Pagba, CM Nevin, A Pavlova, ... The Journal of Physical Chemistry B 121 (15), 3536-3545, 2017 | 18 | 2017 |
