Chen, H.; Fu, H.; Shao, X.; Cai, W. Importance Sampling Methods and Free Energy Calculations. Prog. Chem. 2018, 30 (7), 921-931. https://doi.org/10.7536/PC171026.

Fu, H.; Zhang, H.; Chen, H.; Shao, X.; Chipot, C.; Cai, W. Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys. J. Phys. Chem. Lett. 2018, 9 (16), 4738-4745. https://doi.org/10.1021/acs.jpclett.8b01994.

Chen, H.; Fu, H.; Shao, X.; Chipot, C.; Cai, W. ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines. J. Chem. Inf. Model. 2018, 58, 1315-1318. https://doi.org/10.1021/acs.jcim.8b00115.

Fu, H.; Gumbart, J. C.; Chen, H.; Shao, X.; Cai, W.; Chipot, C. BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations. J. Chem. Inf. Model. 2018, 58 (3), 556-560. https://doi.org/10.1021/acs.jcim.7b00695.

Bonomi, M.; Bussi, G.; Camilloni, C.; Tribello, G. A.; Banáš, P.; Barducci, A.; Bernetti, M.; Bolhuis, P. G.; Bottaro, S.; Branduardi, D.; Capelli, R.; Carloni, P.; Ceriotti, M.; Cesari, A.; Chen, H.; Chen, W.; Colizzi, F.; De, S.; De La Pierre, M.; Donadio, D.; Drobot, V.; Ensing, B.; Ferguson, A. L.; Filizola, M.; Fraser, J. S.; Fu, H.; Gasparotto, P.; Gervasio, F. L.; Giberti, F.; Gil-Ley, A.; Giorgino, T.; Heller, G. T.; Hocky, G. M.; Iannuzzi, M.; Invernizzi, M.; Jelfs, K. E.; Jussupow, A.; Kirilin, E.; Laio, A.; Limongelli, V.; Lindorff-Larsen, K.; Löhr, T.; Marinelli, F.; Martin-Samos, L.; Masetti, M.; Meyer, R.; Michaelides, A.; Molteni, C.; Morishita, T.; Nava, M.; Paissoni, C.; Papaleo, E.; Parrinello, M.; Pfaendtner, J.; Piaggi, P.; Piccini, G.; Pietropaolo, A.; Pietrucci, F.; Pipolo, S.; Provasi, D.; Quigley, D.; Raiteri, P.; Raniolo, S.; Rydzewski, J.; Salvalaglio, M.; Sosso, G. C.; Spiwok, V.; Šponer, J.; Swenson, D. W. H.; Tiwary, P.; Valsson, O.; Vendruscolo, M.; Voth, G. A.; White, A.; The PLUMED consortium. Promoting Transparency and Reproducibility in Enhanced Molecular Simulations. Nat. Methods 2019, 16 (8), 670-673. https://doi.org/10.1038/s41592-019-0506-8.

Chen, H.; Zhang, H.; Shao, X.; Cai, W. Tumbling of Anisole Units in Calixarene Promotes Its Shuttling in Rotaxanes. J. Phys. Chem. C 2019, 123 (29), 18050-18055. https://doi.org/10.1021/acs.jpcc.9b03870.

Fu, H.; Chen, H.; Wang, X.; Chai, H.; Shao, X.; Cai, W.; Chipot, C. Finding an Optimal Pathway on a Multidimensional Free-Energy Landscape. J. Chem. Inf. Model 2020, 60 (11), 5366-5374. https://doi.org/10.1021/acs.jcim.0c00279.

Chen, H.; Maia, J. D. C.; Radak, B. K.; Hardy, D. J.; Cai, W.; Chipot, C.; Tajkhorshid, E. Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD. J. Chem. Inf. Model 2020, 60 (11), 5301-5307. https://doi.org/10.1021/acs.jcim.0c00745.

Fu, H.; Chen, H.; Cai, W.; Shao, X.; Chipot, C. BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations. J. Chem. Inf. Model 2021, 61 (5), 2116-2123. https://doi.org/10.1021/acs.jcim.1c00269.

Fu, H.; Zhang, H.; Chen, H.; Shao, X.; Cai, W. Accurate Estimation of Protein-Ligand Binding Free Energies Based on Geometric Restraints. Acta Chim. Sin. 2021, 79 (4), e472. https://doi.org/10.6023/A20100489.

Chen, H.; Fu, H.; Chipot, C.; Shao, X.; Cai, W. Overcoming Free-Energy Barriers with a Seamless Combination of a Biasing Force and a Collective Variable-Independent Boost Potential. J. Chem. Theory Comput. 2021, 17 (7), 3886-3894. https://doi.org/10.1021/acs.jctc.1c00103.

Chen, H.; Liu, H.; Feng, H.; Fu, H.; Cai, W.; Shao, X.; Chipot, C. MLCV: Bridging Machine-Learning-Based Dimensionality Reduction and Free-Energy Calculation. J. Chem. Inf. Model 2022, 62 (1), 1-8. https://doi.org/10.1021/acs.jcim.1c01010.

Blazhynska, M.; Goulard Coderc de Lacam, E.; Chen, H.; Roux, B.; Chipot, C. Hazardous Shortcuts in Standard Binding Free Energy Calculations. J. Phys. Chem. Lett. 2022, 13 (27), 6250-6258. https://doi.org/10.1021/acs.jpclett.2c01490.

Fu, H.; Chen, H.; Blazhynska, M.; Goulard Coderc de Lacam, E.; Szczepaniak, F.; Pavlova, A.; Shao, X.; Gumbart, J. C.; Dehez, F.; Roux, B.; Cai, W.; Chipot, C. Accurate Determination of Protein:Ligand Standard Binding Free Energies from Molecular Dynamics Simulations. Nat. Protoc. 2022, 17 (4), 1114-1141. https://doi.org/10.1038/s41596-021-00676-1.

Chen, H.; Ogden, D.; Pant, S.; Cai, W.; Tajkhorshid, E.; Moradi, M.; Roux, B.; Chipot, C. A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls. J. Chem. Theory Comput. 2022, 18 (3), 1406-1422. https://doi.org/10.1021/acs.jctc.1c01049.

Coderc de Lacam, E. G.; Blazhynska, M.; Chen, H.; Gumbart, J. C.; Chipot, C. When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy. J. Chem. Theory Comput. 2022, 18 (10), 5890-5900. https://doi.org/10.1021/acs.jctc.2c00604.

Chen, H.; Chipot, C. Enhancing Sampling with Free-Energy Calculations. Curr. Opin. Struct. Biol. 2022, 77, 102497. https://doi.org/10.1016/j.sbi.2022.102497.

Chen, H.; Chipot, C. Chasing Collective Variables Using Temporal Data-Driven Strategies. QRB Discovery 2023, 4, e2. https://doi.org/10.1017/qrd.2022.23.

Chen, H.; Roux, B.; Chipot, C. Discovering Reaction Pathways, Slow Variables, and Committor Probabilities with Machine Learning. J. Chem. Theory Comput. 2023, 19 (14), 4414-4426. https://doi.org/10.1021/acs.jctc.3c00028.

Blazhynska, M.; Goulard Coderc de Lacam, E.; Chen, H.; Chipot, C. Improving Speed and Affordability without Compromising Accuracy: Standard Binding Free-Energy Calculations Using an Enhanced Sampling Algorithm, Multiple-Time Stepping, and Hydrogen Mass Repartitioning. J. Chem. Theory Comput. 2023, 19 (11), 3091-3101. https://doi.org/10.1021/acs.jctc.3c00141.