Haochuan Chen

Publication Activity (10 Years)

Years Active: 2018-2023
Publications (10 Years): 14

Top Topics

Molecular Dynamics

Top Venues

Journal of chemical information and modeling

Journal of chemical theory and computation

The journal of physical chemistry letters

Nature protocols

This page only lists publications with an associated author ORCID identifier.

Publications

Haochuan Chen, Christophe J Chipot
Chasing collective variables using temporal data-driven strategies. QRB discovery 4 (2023)
Haochuan Chen, Benoı T Roux, Christophe J Chipot
Discovering Reaction Pathways, Slow Variables, and Committor Probabilities with Machine Learning. Journal of chemical theory and computation (2023)
Marharyta Blazhynska, Emma Goulard Coderc de Lacam, Haochuan Chen, Christophe J Chipot
Improving Speed and Affordability without Compromising Accuracy: Standard Binding Free-Energy Calculations Using an Enhanced Sampling Algorithm, Multiple-Time Stepping, and Hydrogen Mass Repartitioning. Journal of chemical theory and computation (2023)
Haohao Fu, Haochuan Chen, Marharyta Blazhynska, Emma Goulard Coderc de Lacam, Florence Szczepaniak, Anna Pavlova, Xueguang Shao, James C Gumbart, François Dehez, Benoît Roux, Wensheng Cai, Christophe Chipot
Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations. Nature protocols 17 (4) (2022)
Marharyta Blazhynska, Emma Goulard Coderc de Lacam, Haochuan Chen, Benoı T Roux, Christophe J Chipot
Hazardous Shortcuts in Standard Binding Free Energy Calculations. The journal of physical chemistry letters 13 (27) (2022)
Haochuan Chen, Dylan Ogden, Shashank Pant, Wensheng Cai, Emad Tajkhorshid, Mahmoud Moradi, Benoı T Roux, Christophe J Chipot
A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls. Journal of chemical theory and computation 18 (3) (2022)
Emma Goulard Coderc de Lacam, Marharyta Blazhynska, Haochuan Chen, James C Gumbart, Christophe J Chipot
When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy. Journal of chemical theory and computation 18 (10) (2022)
Haochuan Chen, Haohao Fu, Christophe J Chipot, Xueguang Shao, Wensheng Cai
Overcoming Free-Energy Barriers with a Seamless Combination of a Biasing Force and a Collective Variable-Independent Boost Potential. Journal of chemical theory and computation 17 (7) (2021)
Haochuan Chen, Han Liu, Heying Feng, Haohao Fu, Wensheng Cai, Xueguang Shao, Christophe J Chipot
MLCV: Bridging Machine-Learning-Based Dimensionality Reduction and Free-Energy Calculation. Journal of chemical information and modeling 62 (1) (2021)
Haohao Fu, Haochuan Chen, Wensheng Cai, Xueguang Shao, Christophe J Chipot
BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations. Journal of chemical information and modeling 61 (5) (2021)
Haochuan Chen, Julio D C Maia, Brian K Radak, David J Hardy, Wensheng Cai, Christophe J Chipot, Emad Tajkhorshid
Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD. Journal of chemical information and modeling 60 (11) (2020)
Haohao Fu, Haochuan Chen, Xin'ao Wang, Hao Chai, Xueguang Shao, Wensheng Cai, Christophe J Chipot
Finding an Optimal Pathway on a Multidimensional Free-Energy Landscape. Journal of chemical information and modeling 60 (11) (2020)
Haohao Fu, Hong Zhang, Haochuan Chen, Xueguang Shao, Christophe J Chipot, Wensheng Cai
Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys. The journal of physical chemistry letters 9 (16) (2018)
Haochuan Chen, Haohao Fu, Xueguang Shao, Christophe J Chipot, Wensheng Cai
ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines. Journal of chemical information and modeling 58 (7) (2018)