Total citations 1429 as of 2018/12/29; H-index = 14.
* markes out all corresponding authors.

Journal Articles

  1. Gerhard Konig,* Frank Pickard, Jing Huang, Walter Thiel, Alexander MacKerell, Bernard 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)

  2. 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)

  3. 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)

  4. 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)

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

  6. 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)

  7. 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)

  8. 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)

  9. 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)

  10. 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)

  11. 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)

  12. 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)

  13. 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)

  14. 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)

  15. 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)

  16. 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)

  17. 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)

  18. 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)

  19. 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)

  20. 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)

  21. 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)

  22. 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)

  23. 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)

  24. 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)

  25. 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)

  26. 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)

  27. 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)

  28. 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)

  29. 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)

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

  31. 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)

  32. 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)

  33. 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)