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Anna Pavlova
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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
2072016
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
1562020
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
982019
Understanding the Role of Water in Aqueous Ruthenium‐Catalyzed Transfer Hydrogenation of Ketones.
A Pavlova, EJ Meijer
ChemPhysChem 13 (15), 3492-3496, 2012
812012
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
602022
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
592021
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
482021
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
422016
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
392022
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
352013
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
262021
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
252018
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
232021
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
212016
Parametrization of macrolide antibiotics using the force field toolkit
A Pavlova, JC Gumbart
Journal of computational chemistry 36 (27), 2052-2063, 2015
202015
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
152017
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
132020
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
122022
Toward the rational design of macrolide antibiotics to combat resistance
A Pavlova, JM Parks, AK Oyelere, JC Gumbart
Chemical Biology & Drug Design 90 (5), 641-652, 2017
112017
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
92022
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