Total citations 6249 as of 2022/06/18; H-index = 22.
# denotes equal contributions, * markes out all corresponding authors.

Submitted Manuscripts and Preprints

Direct Measurement of Gln-Phe NH-π interactions in Protein

A Thermodynamic Investigation of Amyloid Precursor Protein Processing by Human γ-Secretase

Mechanism of Substrate Transport of the Human Heteromeric Amino Acid Transporter y+LAT1-4F2hc Complex

Journal Articles

  1. Tengyu Xie#, Ximin Chi#, Bangdong Huang, Fangfei Ye, Qiang Zhou*, and Jing Huang*
    Rational Exploration of Fold Atlas for Human Solute Carrier Proteins
    Structure, in press

  2. Jing Huang
    Editorial: Special Issue on Polarizable Force Fields for Biomolecular Modelling
    J. Comput. Biophys. Chem. 4, 389 (2022)

  3. Jianhua Luo#, Qi Yang#, Xiaofeng Zhang#, Yuanyuan Zhang#, Li Wan#, Xiechao Zhan, Yao Zhou, Liuqing He, Danyang Li, Dazhi Jin, Ying Zhen, Jing Huang, Yanyan Li*, and Liang Tao*
    TFPI is a Colonic Crypt Receptor for TcdB from Hypervirulent Clade 2 C. difficile
    Cell, 185, 980 (2022)

  4. Wenyi Zhang and Jing Huang*
    EViS: an Enhanced Virtual Screening Approach based on Pocket-Ligand Similarity
    J. Chem. Inf. Model., 62, 498 (2022)

  5. Qiaozhu Tan, Ye Ding, Zongyang Qiu, and Jing Huang*
    Binding Energy and Free Energy of Calcium Ion to Calmodulin EF-hands with the Drude Polarizable Force Field
    ACS Phys. Chem. Au, 2, 143 (2022)

  6. Abhishek A. Kognole#, Jumin Lee#, Sang‐Jun Park#, Sunhwan Jo#, Payal Chatterjee, Justin A. Lemkul, Jing Huang, Alexander D. MacKerell Jr.*, and Wonpil Im*
    CHARMM-GUI Drude Prepper for Molecular Dynamics Simulation Using the Classical Drude Polarizable Force Field
    J. Comput. Chem., 43, 359 (2022)

  7. Francois A. Thelot, Wenyi Zhang, KangKang Song, Chen Xu, Jing Huang, and Maofu Liao*
    Distinct Allosteric Mechanisms of First-generation MsbA Inhibitors
    Science, 374, 580 (2021)

  8. Zhijun Pan, Jing Huang*, and Wei Zhuang*
    Protein-Ligand Binding Molecular Details Revealed by Terahertz Optical Kerr Spectroscopy: A Simulation Study
    JACS Au, 1, 1788 (2021)

  9. Xiaoliang Pan, Junjie Yang, Richard Van, Evgeny Epifanovsky, Junming Ho, Jing Huang, Jingzhi Pu*, Ye Mei*, Kwangho Nam*, and Yihan Shao*
    Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions
    J. Chem. Theo. Comput., 17, 5745 (2021)

  10. You Xu and Jing Huang*
    Validating the CHARMM36m Protein Force Field with LJ-PME Reveals Altered Hydrogen Bonding Dynamics under Elevated Pressures
    Commun. Chem., 4, 99 (2021)

  11. Chengwei Zhang and Jing Huang*
    Interactions between Nucleosomes: From Atomistic Simulation to Polymer Model
    Front. Mol. Biosci., 8, 624679 (2021)
    special issue “Advanced Sampling and Modeling in Molecular Simulations for Slow and Large-Scale Biomolecular Dynamics”

  12. Jian Zhu and Jing Huang*
    Methylguanidinium at the Air/Water Interface: A Simulation Study with the Drude Polarizable Force Field
    J. Phys. Chem. B, 125, 393 (2021)

  13. Jinghui Zhang, Zongyang Qiu, Jiahua Fan, Fang He, Wenyuan Kang, Sihui Yang, Hong-hui Wang*, Jing Huang*, and Zhou Nie*
    Scan and Unlock: a Programmable DNA Molecular Automaton for Cell-specific Modulation of a Signaling Ligand-receptor Interaction
    Angew. Chem. Int. Ed., 60, 6733 (2021)

  14. Shuai Wang#, Zongyang Qiu#, Yingnan Hou#, Xiya Deng#, Wei Xu#, Tingting Zheng, Peihan Wu, Shaofang Xie, Weixiang Bian, Chong Zhang, Zewei Sun, Kunpeng Liu, Chao Shan, Aifu Lin, Shibo Jiang, Youhua Xie, Qiang Zhou, Lu Lu*, Jing Huang*, and Xu Li*
    AXL is a Candidate Receptor for SARS-CoV-2 that Promotes Infection of Pulmonary and Bronchial Epithelial Cells
    Cell Research, 31, 126 (2021)

  15. Ximin Chi#, Xueqing Jin#, Yun Chen#, Xiaoli Lu#, Xinyu Tu, Xiaorong Li, Yuanyuan Zhang, Jianlin Lei, Jing Huang, Zhuo Huang*, Qiang Zhou*, and Xiaojing Pan*
    Structural Insights into the Gating Mechanism of Human SLC26A9 Mediated by its C-terminal Sequence
    Cell Discovery, 6, 55 (2020)

  16. Fang-Yu Lin, Jing Huang, Poonam Pandey, Chetan Rupakheti, Jing Li, Benoit Roux, and Alexander D. MacKerell Jr.*
    Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field
    J. Chem. Theo. Comput., 16, 3221 (2020)

  17. Renhong Yan#, Yaning Li#, Yi Shi#, Jiayao Zhou, Jianlin Lei, Jing Huang*, and Qiang Zhou*
    Cryo-EM Structure of the Human Heteromeric Amino Acid Transporter b0,+AT-rBAT
    Science Advances, 6, eaay6379 (2020)

  18. Ye Ding, You Xu, Cheng Qian, Jinfeng Chen, Jian Zhu, Houhou Huang, Yi Shi, and Jing Huang*
    Predicting Partition Coefficients of Drug-like Molecules in the SAMPL6 Challenge with Drude Polarizable Force Fields
    J. Comput. Aided Mol. Des., 34, 421 (2020)

  19. Andreas Kramer,* Frank C. Pickard IV, Jing Huang, Richard M. Venable, Andrew C. Simmonett, Dirk Reith, Karl N Kirschner, Richard W. Pastor, and Bernard R. Brooks
    Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects
    J. Chem. Theo. Comput., 15, 3854 (2019)

  20. Gerhard Konig,* Frank C. Pickard IV, Jing Huang, Walter Thiel, Alexander D. MacKerell Jr., Bernard R. Brooks, and Darrin York*
    A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes
    Molecules, 23, 2695 (2018)

  21. Samarjeet Prasad,* Jing Huang, Qiao Zeng, and Bernard R. Brooks
    An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge
    J. Comput. Aided Mol. Des., 32, 1191 (2018)

  22. Jing Huang, Justin A. Lemkul, Peter Eastman, and Alexander D. MacKerell Jr.*
    Molecular Dynamics Simulations Using the Drude Polarizable Force Field on GPUs with OpenMM: Implementation, Validation, and Benchmarks
    J. Comput. Chem., 39, 1682 (2018)

  23. Alison N. Leonard, Andrew C. Simmonett, Frank C. Pickard IV, Jing Huang, Richard M. Venable, Jeffery B. Klauda, Bernard R. Brooks, and Richard W. Pastor*
    Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions using Alkane Simulations
    J. Chem. Theo. Comput., 14, 948 (2018)

  24. Jing Huang and Alexander D. MacKerell Jr.*
    Force Field Development and Simulations of Intrinsically Disordered Proteins
    Curr. Opin. Struct. Biol., 48, 40 (2018)

  25. Jing Huang,* Andrew C. Simmonett, Frank C. Pickard IV, Alexander D. MacKerell Jr., and Bernard R. Brooks
    Mapping the Drude Polarizable Force Field onto a Multipole and Induced Dipole Model
    J. Chem. Phys., 147, 161702 (2017)

  26. Mingjun Yang, Jing Huang, Raphael Simon, Lai-Xi Wang, and Alexander D. MacKerell Jr.*
    Conformational Heterogeneity of the HIV Envelope Glycan Shield
    Sci. Report, 7, 4435 (2017)

  27. Jing Huang, Ye Mei, Gerhard Konig, Andrew C. Simmonett, Frank C. Pickard IV, Qin Wu, Lee-Ping Wang, Alexander D. MacKerell Jr., Bernard R. Brooks, and Yihan Shao*
    An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches
    J. Chem. Theo. Comput., 13, 679 (2017)

  28. Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, Ting Ran, Michael Feig, Bert L. de Groot, Helmut Grubmueller, and Alexander D. MacKerell Jr.*
    CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins
    Nature Methods, 14, 71 (2017)

  29. Florentina Tofoleanu,* Juyong Lee, Gerhard Konig, Frank C. Pickard IV, Jing Huang, Minkyung Baek, Chaok Seok, and Bernard R. Brooks
    Absolute binding free energy calculations for octa-acids and guests in SAMPL5: Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge
    J. Comput. Aided Mol. Des., 31, 107 (2017)

  30. Juyong Lee,* Florentina Tofoleanu, Gerhard Konig, Frank C. Pickard IV, Jing Huang, Ana Damjanovic, Minkyung Baek, Chaok Seok, and Bernard R. Brooks
    Absolute binding free energy calculations of CBClip-guest systems in the SAMPL5 blind challenge
    J. Comput. Aided Mol. Des., 31, 71 (2017)

  31. Gerhard Konig,* Frank C. Pickard IV, Jing Huang, Andrew C. Simmonett, Florentina Tofoleanu, Juyong Lee, Pavlo O. Dral, Samarjeet Prasad, Michael Jones, Yihan Shao, Walter Thiel, and Bernard R. Brooks
    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
    J. Comput. Aided Mol. Des., 30, 989 (2016)

  32. Jing Huang, Sirish Kaushik Lakkaraju, Andrew Coop, and Alexander D. MacKerell Jr.*
    Conformational Heterogeneity of Intracellular Loop 3 of the µ-Opioid G-Protein Coupled Receptor
    J. Phys. Chem. B, 120, 11897 (2016)

  33. Jamal Chauhan, Steven Cardinale, Lei Fang, Jing Huang, Steven M. Kwasny, M. Ross Pennington, Kelly Basi, Robert diTargiani, Benedict R. Capacio, Alexander D. MacKerell Jr., Timothy J. Opperman, Steven Fletcher, and Erik P. H. de Leeuw*
    Towards Development of Small Molecule Lipid II Inhibitors as Novel Antibiotics
    PLoS ONE, 11, e0164515 (2016)

  34. Yuan Feng, Jing Huang, Seongheun Kim, Jihyun Shim, Alexander D. MacKerell Jr., and Nien-Hui Ge*
    Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation
    J. Phys. Chem. B, 120, 5325 (2016)

  35. Justin A. Lemkul, Jing Huang, Benoit Roux, and Alexander D. MacKerell Jr.*
    An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications
    Chem. Rev., 116, 4983 (2016)

  36. Sirish Kaushik Lakkaraju, Justin A. Lemkul, Jing Huang, and Alexander D. MacKerell Jr.*
    DIRECT-ID: An automated method to identify and quantify conformational variations—application to β2-adrenergic GPCR
    J. Comp. Chem., 37, 416 (2016)

  37. Justin A. Lemkul, Jing Huang, and Alexander D. MacKerell Jr.*
    Induced Dipole-Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides
    J. Phys. Chem. B, 119, 15574 (2015)

  38. Mingjun Yang, Jing Huang, and Alexander D. MacKerell Jr.*
    Enhanced Conformational Sampling Using Replica Exchange with Concurrent Solute Scaling and Hamiltonian Biasing Realized in One Dimension
    J. Chem. Theo. Comput., 11, 2855 (2015)

  39. Daryl L. Howard, Henrik G. Kjaergaard,* Jing Huang, and Markus Meuwly*
    Infrared and near Infrared Spectroscopy of Acetylacetone and Hexafluoroacetylacetone
    J. Phys. Chem. A, 119, 7980 (2015)

  40. Steven Fletcher, Wenbo Yu, Jing Huang, Steven M. Kwasny, Jay Chauhan, Timothy J. Opperman, Alexander D. MacKerell Jr., and Erik P. H. de Leeuw*
    Structure–activity exploration of a small-molecule Lipid II inhibitor
    Drug Des. Devel. Ther., 9, 2383 (2015)

  41. Jing Huang, Pedro E. M. Lopes, Benoit Roux and Alexander D. MacKerell Jr.*
    Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model
    J. Phys. Chem. Lett., 5, 3144 (2014)

  42. Jing Huang and Alexander D. MacKerell Jr.*
    Induction of Peptide Bond Dipoles Drives Cooperative Helix Formation in the (AAQAA)3 Peptide
    Biophys. J., 107, 991 (2014)

  43. Jing Huang, Marcin Buchowiechi, Tibor Nagy, Jiri Vanicek* and Markus Meuwly*
    Kinetic Isotope Effect in Malonaldehyde from Path Integral Monte Carlo Simulations
    Phys. Chem. Chem. Phys., 16, 204 (2014)

  44. Pedro E. M. Lopes, Jing Huang, Jihyun Shim, Yun Luo, Hui Li, Benoit Roux, and Alexander D. MacKerell Jr.*
    Polarizable Force Field for Peptides and Proteins based on the Classical Drude Oscillator
    J. Chem. Theo. Comput., 9, 5430 (2013)

  45. Kristen M. Varney, Alexandre M. J. J. Bonvin, Marzena Pazgier, Jakob Malin, Wenbo Yu, Eugene Ateh, Taiji Oashi, Wuyuan Lu, Jing Huang, Marlies Diepeveen-de Buin, Joseph Bryant, Eefjan Breukink, Alexander D. MacKerell Jr., and Erik P. H. de Leeuw*
    Turning Defense into Offense: Defensin Mimetics as Novel Antibiotics Targeting Lipid II
    PLoS Pathog., 9, e1003732 (2013)

  46. Jing Huang and Alexander D. MacKerell Jr.*
    CHARMM36 All-Atom Additive Protein Force Field: Validation Based on Comparison to NMR Data
    J. Comp. Chem., 34, 2135 (2013)

  47. Jing Huang, Daniel Haeussinger, Urs Gellrich, Wolfgang Seiche, Bernhard Breit, and Markus Meuwly*
    Hydrogen-Bond and Solvent Dynamics in Transition Metal Complexes: a Combined Simulation and NMR-Investigation
    J. Phys. Chem. B, 116, 14406 (2012)

  48. Pierre-Andre Cazade, Jing Huang, Juvenal Yosa, Jaroslaw J. Szymczak and Markus Meuwly*
    Atomistic Simulations of Reactive Processes in the Gas- and Condensed-Phase
    Int. Rev. Phys. Chem., 31, 235 (2012)

  49. Jing Huang and Markus Meuwly*
    Force Field Refinement from NMR Scalar Couplings
    Chem. Phys., 396, 116 (2012)

  50. Urs Gellrich, Jing Huang, Wolfgang Seiche, Manfred Keller, Markus Meuwly* and Bernhard Breit*
    Ligand Self-Assembling through Complementary Hydrogen-Bonding in the Coordination Sphere of a Transition Metal Center: The 6-Diphenylphosphanylpyridin-2(1H)-one System
    J. Am. Chem. Soc., 133, 964 (2011)

  51. Jing Huang and Markus Meuwly*
    Explicit Hydrogen-bond Potentials and their Application to NMR Scalar Couplings in Proteins
    J. Chem. Theo. Comput., 6, 467 (2010)

  52. Jing Huang and Guozhen Wu*
    Dynamical Potential Approach to DCO Highly Excited Vibration
    Chem. Phys. Lett., 439, 231 (2007)

Book Chapters:

  1. Jing Huang and Markus Meuwly*
    Force Field Treatment of Proton and Hydrogen Transfer in Molecular Systems
    Chapter 10 in “Tautomerism: Methods and Theories”, Ed: L. Antonov, Wiley, 253-276 (2013)

  2. Jing Huang, Michael Devereux, Franziska Hofmann, and Markus Meuwly*
    Computational Organometallic Chemistry with Force Fields
    Chapter 2 in “Computational Organometallic Chemistry”, Ed: O. Wiest and Y. Wu, Springer, 19-46 (2012)