CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data. - Jing Huang 004; Alexander D. MacKerell Jr. (J. Comput. Chem., 2013)

Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge. - Gerhard König; Frank C. Pickard IV; Jing Huang 004; Andrew C. Simmonett; Florentina Tofoleanu; Juyong Lee; Pavlo O. Dral; Samarjeet Prasad; Michael R. Jones; Yihan Shao; Walter Thiel; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2016)

DIRECT-ID: An automated method to identify and quantify conformational variations - application to β2-adrenergic GPCR. - Sirish Kaushik Lakkaraju; Justin A. Lemkul; Jing Huang 004; Alexander D. MacKerell Jr. (J. Comput. Chem., 2016)

Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge. - Juyong Lee; Florentina Tofoleanu; Frank C. Pickard IV; Gerhard König; Jing Huang 004; Ana Damjanovic; Minkyung Baek; Chaok Seok; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2017)

Absolute binding free energies for octa-acids and guests in SAMPL5 - Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge. - Florentina Tofoleanu; Juyong Lee; Frank C. Pickard IV; Gerhard König; Jing Huang 004; Minkyung Baek; Chaok Seok; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2017)

An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge. - Samarjeet Prasad; Jing Huang 004; Qiao Zeng; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2018)

Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks. - Jing Huang 004; Justin A. Lemkul; Peter K. Eastman; Alexander D. MacKerell Jr. (J. Comput. Chem., 2018)

Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields. - Ye Ding; You Xu; Cheng Qian; Jinfeng Chen; Jian Zhu; Houhou Huang; Yi Shi; Jing Huang 004 (J. Comput. Aided Mol. Des., 2020)

CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. - Abhishek A. Kognole; Jumin Lee; Sang-Jun Park; Sunhwan Jo; Payal Chatterjee; Justin A. Lemkul; Jing Huang 004; Alexander D. MacKerell Jr.; Wonpil Im (J. Comput. Chem., 2022)

EViS: An Enhanced Virtual Screening Approach Based on Pocket-Ligand Similarity. - Wenyi Zhang; Jing Huang 004 (J. Chem. Inf. Model., 2022)

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. - Peter K. Eastman; Raimondas Galvelis; Raúl P. Peláez; Charlles R. A. Abreu; Stephen E. Farr; Emilio Gallicchio; Anton Gorenko; Michael M. Henry; Frank Hu; Jing Huang 004; Andreas Krämer; Julien Michel; et al. (CoRR, 2023)

Constant advance replicas method for locating minimum energy paths and transition states. - Zilin Song; Ye Ding; Jing Huang 004 (J. Comput. Chem., 2023)

A Simple Way to Incorporate Target Structural Information in Molecular Generative Models. - Wenyi Zhang; Kaiyue Zhang; Jing Huang 004 (J. Chem. Inf. Model., 2023)

Alchemical Transformations and Beyond: Recent Advances and Real-World Applications of Free Energy Calculations in Drug Discovery. - Runtong Qian; Jing Xue; You Xu; Jing Huang 004 (J. Chem. Inf. Model., 2024)

Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters? - Tengyu Xie; Jing Huang 004 (J. Chem. Inf. Model., 2024)