Articles with public access mandates - Haochuan ChenLearn more
Not available anywhere: 7
BFEE2: automated, streamlined, and accurate absolute binding free-energy calculations
H Fu, H Chen, W Cai, X Shao, C Chipot
Journal of Chemical Information and Modeling 61 (5), 2116-2123, 2021
Mandates: National Natural Science Foundation of China, Agence Nationale de la Recherche
Overcoming free-energy barriers with a seamless combination of a biasing force and a collective variable-independent boost potential
H Chen, H Fu, C Chipot, X Shao, W Cai
Journal of Chemical Theory and Computation 17 (7), 3886-3894, 2021
Mandates: National Natural Science Foundation of China, Agence Nationale de la Recherche
MLCV: Bridging machine-learning-based dimensionality reduction and free-energy calculation
H Chen, H Liu, H Feng, H Fu, W Cai, X Shao, C Chipot
Journal of Chemical Information and Modeling 62 (1), 1-8, 2021
Mandates: National Natural Science Foundation of China, Agence Nationale de la Recherche
Hazardous shortcuts in standard binding free energy calculations
M Blazhynska, E Goulard Coderc de Lacam, H Chen, B Roux, C Chipot
The Journal of Physical Chemistry Letters 13 (27), 6250-6258, 2022
Mandates: US National Science Foundation, Agence Nationale de la Recherche
ELF: an extended-Lagrangian free energy calculation module for multiple molecular dynamics engines
H Chen, H Fu, X Shao, C Chipot, W Cai
Journal of chemical information and modeling 58 (7), 1315-1318, 2018
Mandates: National Natural Science Foundation of China
Improving Speed and Affordability without Compromising Accuracy: Standard Binding Free-Energy Calculations Using an Enhanced Sampling Algorithm, Multiple-Time Stepping, and …
M Blazhynska, E Goulard Coderc de Lacam, H Chen, C Chipot
Journal of Chemical Theory and Computation 19 (11), 3091-3101, 2023
Mandates: Agence Nationale de la Recherche
Tumbling of anisole units in calixarene promotes its shuttling in rotaxanes
H Chen, H Zhang, X Shao, W Cai
The Journal of Physical Chemistry C 123 (29), 18050-18055, 2019
Mandates: National Natural Science Foundation of China
Available somewhere: 13
Zooming across the free-energy landscape: shaving barriers, and flooding valleys
H Fu, H Zhang, H Chen, X Shao, C Chipot, W Cai
The journal of physical chemistry letters 9 (16), 4738-4745, 2018
Mandates: National Natural Science Foundation of China
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
Mandates: US National Science Foundation, US National Institutes of Health, National …
BFEE: A user-friendly graphical interface facilitating absolute binding free-energy calculations
H Fu, JC Gumbart, H Chen, X Shao, W Cai, C Chipot
Journal of chemical information and modeling 58 (3), 556-560, 2018
Mandates: US National Science Foundation, US National Institutes of Health, National …
Finding an optimal pathway on a multidimensional free-energy landscape
H Fu, H Chen, X Wang, H Chai, X Shao, W Cai, C Chipot
Journal of Chemical Information and Modeling 60 (11), 5366-5374, 2020
Mandates: National Natural Science Foundation of China, Agence Nationale de la Recherche
Boosting free-energy perturbation calculations with GPU-accelerated NAMD
H Chen, JDC Maia, BK Radak, DJ Hardy, W Cai, C Chipot, E Tajkhorshid
Journal of chemical information and modeling 60 (11), 5301-5307, 2020
Mandates: US National Institutes of Health, Agence Nationale de la Recherche
Discovering reaction pathways, slow variables, and committor probabilities with machine learning
H Chen, B Roux, C Chipot
Journal of Chemical Theory and Computation 19 (14), 4414-4426, 2023
Mandates: US National Science Foundation, US National Institutes of Health, Agence …
Enhancing sampling with free-energy calculations
H Chen, C Chipot
Current Opinion in Structural Biology 77, 102497, 2022
Mandates: Agence Nationale de la Recherche
A companion guide to the string method with swarms of trajectories: Characterization, performance, and pitfalls
H Chen, D Ogden, S Pant, W Cai, E Tajkhorshid, M Moradi, B Roux, ...
Journal of Chemical Theory and Computation 18 (3), 1406-1422, 2022
Mandates: US National Science Foundation, US National Institutes of Health, National …
When the dust has settled: calculation of binding affinities from first principles for SARS-CoV-2 variants with quantitative accuracy
EG Coderc de Lacam, M Blazhynska, H Chen, JC Gumbart, C Chipot
Journal of Chemical Theory and Computation 18 (10), 5890-5900, 2022
Mandates: US National Science Foundation, Agence Nationale de la Recherche
Chasing collective variables using temporal data-driven strategies
H Chen, C Chipot
QRB discovery 4, e2, 2023
Mandates: Agence Nationale de la Recherche
A Rigorous Framework for Calculating Protein–Protein Binding Affinities in Membranes
M Blazhynska, JC Gumbart, H Chen, E Tajkhorshid, B Roux, C Chipot
Journal of Chemical Theory and Computation 19 (24), 9077-9092, 2023
Mandates: US National Science Foundation, US National Institutes of Health, Agence …
Accurate Estimation of Protein-ligand Binding Free Energies Based on Geometric Restraints
F Haohao, C Haochuan, Z Hong, S Xueguang, C Wensheng
Acta Chimica Sinica 79 (4), 472, 2021
Mandates: National Natural Science Foundation of China
Expanded functionality and portability for the Colvars library
G Fiorin, F Marinelli, LR Forrest, H Chen, C Chipot, A Kohlmeyer, ...
The Journal of Physical Chemistry B 128 (45), 11108-11123, 2024
Mandates: European Commission, Agence Nationale de la Recherche
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