| Alchemical binding free energy calculations in AMBER20: Advances and best practices for drug discovery TS Lee, BK Allen, TJ Giese, Z Guo, P Li, C Lin, TD McGee Jr, ... Journal of Chemical Information and Modeling 60 (11), 5595-5623, 2020 | 280 | 2020 |
| Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semi-empirical reference potential. I. Weighted thermodynamics … P Li, X Jia, X Pan, Y Shao, Y Mei Journal of chemical theory and computation 14 (11), 5583-5596, 2018 | 61 | 2018 |
| Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi … X Pan, P Li, J Ho, J Pu, Y Mei, Y Shao Physical Chemistry Chemical Physics 21 (37), 20595-20605, 2019 | 44 | 2019 |
| Efficient strategy for the calculation of solvation free energies in water and chloroform at the quantum mechanical/molecular mechanical level M Wang, P Li, X Jia, W Liu, Y Shao, W Hu, J Zheng, BR Brooks, Y Mei Journal of Chemical Information and Modeling 57 (10), 2476-2489, 2017 | 36 | 2017 |
| Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 4 … JN Wang, W Liu, P Li, Y Mo, W Hu, J Zheng, X Pan, Y Shao, Y Mei Journal of chemical theory and computation 17 (3), 1318-1325, 2021 | 22 | 2021 |
| Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 3 … W Hu, P Li, JN Wang, Y Xue, Y Mo, J Zheng, X Pan, Y Shao, Y Mei Journal of chemical theory and computation 16 (11), 6814-6822, 2020 | 18 | 2020 |
| Solvation Free Energy Calculation Using a Fixed-Charge Model: Implicit and Explicit Treatments of the Polarization Effect X Jia, P Li The Journal of Physical Chemistry B 123 (5), 1139-1148, 2019 | 13 | 2019 |
| Computational insights into endo/exo selectivity of the diels–alder reaction in explicit solvent at ab initio quantum mechanical/molecular mechanical level P Li, F Liu, Y Shao, Y Mei The Journal of Physical Chemistry B 123 (24), 5131-5138, 2019 | 12 | 2019 |
| Efficient computation of free energy surfaces of Diels–Alder reactions in explicit solvent at ab initio QM/MM level P Li, F Liu, X Jia, Y Shao, W Hu, J Zheng, Y Mei Molecules 23 (10), 2487, 2018 | 12 | 2018 |
| Calculations of the absolute binding free energies for Ralstonia solanacearum lectins bound with methyl-α-l-fucoside at molecular mechanical and quantum mechanical/molecular … W Liu, X Jia, M Wang, P Li, X Wang, W Hu, J Zheng, Y Mei RSC advances 7 (61), 38570-38580, 2017 | 12 | 2017 |
| Precise binding free energy calculations for multiple molecules using an optimal measurement network of pairwise differences P Li, Z Li, Y Wang, H Dou, BK Radak, BK Allen, W Sherman, H Xu Journal of Chemical Theory and Computation 18 (2), 650-663, 2021 | 10 | 2021 |
| Discovery of SBF1 as an allosteric inhibitor targeting the PIF-pocket of 3-phosphoinositide-dependent protein kinase-1 W Liu, P Li, Y Mei Journal of Molecular Modeling 25 (7), 187, 2019 | 9 | 2019 |
| Perspective: Reference-Potential Methods for the Study of Thermodynamic Properties in Chemical Processes: Theory, Applications, and Pitfalls JN Wang, Y Xue, P Li, X Pan, M Wang, Y Shao, Y Mo, Y Mei The Journal of Physical Chemistry Letters 14, 4866–4875, 2023 | 4 | 2023 |
| Comparison of Accuracy and Convergence Rate between Equilibrium and Nonequilibrium Alchemical Transformations for Calculation of Relative Binding Free Energy P Li, X Jia, M Wang, Y Mei Chinese Journal of Chemical Physics 30 (6), 789-799, 2017 | 3 | 2017 |
| Potent inhibitors targeting cyclin-dependent kinase 9 discovered via virtual high-throughput screening and absolute binding free energy calculations S Wang, F Liu, P Li, JN Wang, Y Mo, B Lin, Y Mei Physical Chemistry Chemical Physics 26 (6), 5377-5386, 2024 | 1 | 2024 |
| Selectivity of parvalbumin B protein binding to Ca2+ and Mg2+ at an ab initio QM/MM level using the reference-potential method S Jin, JN Wang, Y Xue, P Li, Y Mei Chinese Journal of Chemical Physics 34 (6), 741-750, 2021 | 1 | 2021 |
| FEP-SPell-ABFE: An Open-Source Automated Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery P Li, T Pu, Y Mei | | 2024 |
| Structures of the Mycobacterium tuberculosis efflux pump EfpA reveal the mechanisms of transport and inhibition S Wang, K Wang, K Song, ZW Lai, P Li, D Li, Y Sun, Y Mei, C Xu, M Liao Nature Communications 15 (1), 7710, 2024 | | 2024 |
Ye Mei (梅晔)East China Normal UniversityVerified email at phy.ecnu.edu.cn