28 peer-reviewed journal articles and 2 book chapters, including 14 first-author ones. Total citations 698 as of 2017/09/14.

Manuscripts under Review
Force Field Development and Simulations of Intrinsically Disordered Proteins
J. Huang and A. MacKerell Jr.

Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions using Alkane Simulations
A. Leonard, A. Simmonett, F. Pickard, J. Huang, R. Venable, J. Klauda, B. Brooks, and R. Pastor

Journal Articles

  1. J. Huang, A. Simmonett, F. Pickard, A. MacKerell Jr., and B. Brooks
    Mapping the Drude Polarizable Force Field onto a Multipole and Induced Dipole Model
    J. Chem. Phys., 147, 161702 (2017)

  2. M. Yang, J. Huang, R. Simon, L.-X. Wang, and A. MacKerell Jr.
    Conformational Heterogeneity of the HIV Envelope Glycan Shield
    Sci. Report, 7, 4435 (2017)

  3. J. Huang, Y. Mei, G. Konig, A. Simmonett, F. Pickard, Q. Wu, L.-P. Wang, A. MacKerell Jr., B. Brooks, and Y. 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)

  4. J. Huang, S. Rauscher, G. Nawrocki, T. Ran, M. Feig, B. de Groot, H. Grubmueller, and A. MacKerell Jr.
    CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins
    Nature Methods, 14, 71 (2017)

  5. F. Tofoleanu, J. Lee, G. Konig, F. Pickard, J. Huang, M. Baek, C. Seok, and B. 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)

  6. J. Lee, F. Tofoleanu, G. Konig, F. Pickard, J. Huang, A. Damjanovic, M. Baek, C. Seok, and B. Brooks
    Absolute binding free energy calculations of CBClip-guest systems in the SAMPL5 blind challenge
    J. Comput. Aided Mol. Des., 31, 71 (2017)

  7. G. Konig, F. Pickard, J. Huang, A. Simmonett, F. Tofoleanu, J. Lee, P. Dral, F. Samarjeet, M. Jones, Y. Shao, W. Thiel, and B. 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)

  8. J. Huang, S. K. Lakkaraju, A. Coop, and A. MacKerell Jr.
    Conformational Heterogeneity of Intracellular Loop 3 of the µ-Opioid G-Protein Coupled Receptor
    J. Phys. Chem. B, 120, 11897 (2016)

  9. J. Chauhan, S. Cardinale, L. Fang, J. Huang, S. Kwasny, M. Pennington, K. Basi, R. diTargiani, B. Capacio, T. Opperman, A. MacKerell Jr., T. Opperman, S. Fletcher, and E. de Leeuw
    Towards Development of Small Molecule Lipid II Inhibitors as Novel Antibiotics
    PLoS ONE, 11, e0164515 (2016)

  10. Y. Feng, J. Huang, S. Kim, J. Shim, A. MacKerell Jr., and N.-H. Ge
    Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation
    J. Phys. Chem. B, 120, 5325 (2016)

  11. J. Lemkul, J. Huang, B. Roux, and A. MacKerell Jr.
    An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications
    Chem. Rev., 116, 4983 (2016)

  12. S. K. Lakkaraju, J. Lemkul, J. Huang, and A. MacKerell Jr.
    DIRECT-ID: An automated method to identify and quantify conformational variations—application to β2-adrenergic GPCR
    J. Comp. Chem., 37, 416 (2016)

  13. J. Lemkul, J. Huang, and A. 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)

  14. M. Yang, J. Huang, and A. 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)

  15. D. Howard, H. Kjaergaard, J. Huang, and M. Meuwly
    Infrared and near Infrared Spectroscopy of Acetylacetone and Hexafluoroacetylacetone
    J. Phys. Chem. A, 119, 7980 (2015)

  16. S. Fletcher, W. Yu, J. Huang, S. Kwasny, J. Chauhan, T. Opperman, A. MacKerell Jr., and E. de Leeuw
    Structure–activity exploration of a small-molecule Lipid II inhibitor
    Drug Des. Devel. Ther., 9, 2383 (2015)

  17. J. Huang, P. Lopes, B. Roux and A. 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)

  18. J. Huang and A. MacKerell Jr.
    Induction of Peptide Bond Dipoles Drives Cooperative Helix Formation in the (AAQAA)3 Peptide
    Biophys. J., 107, 991 (2014)

  19. J. Huang, M. Buchowiechi, T. Nagy, J. Vanicek and M. Meuwly
    Kinetic Isotope Effect in Malonaldehyde from Path Integral Monte Carlo Simulations
    Phys. Chem. Chem. Phys., 16, 204 (2014)

  20. P. Lopes, J. Huang, J. Shim, Y. Luo, H. Li, B. Roux, and A. MacKerell Jr.
    Polarizable Force Field for Peptides and Proteins based on the Classical Drude Oscillator
    J. Chem. Theo. Comput., 9, 5430 (2013)

  21. K. Varney, A. Bonvin, M. Pazgier, J. Malin, W. Yu, E. Ateh, T. Oashi, W. Lu, J. Huang, M. de Buin, J. Bryant, E. Breukink, A. MacKerell Jr., and E. de Leeuw
    Turning Defense into Offense: Defensin Mimetics as Novel Antibiotics Targeting Lipid II
    PLoS Pathog., 9, e1003732 (2013)

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

  23. J. Huang, D. Haeussinger, U. Gellrich, W. Seiche, B. Breit, and M. Meuwly
    Hydrogen-Bond and Solvent Dynamics in Transition Metal Complexes: a Combined Simulation and NMR-Investigation
    J. Phys. Chem. B, 116, 14406 (2012)

  24. P.-A. Cazade, J. Huang, J. Yosa, J. J. Szymczak and M. Meuwly
    Atomistic Simulations of Reactive Processes in the Gas- and Condensed-Phase
    Int. Rev. Phys. Chem., 31, 235 (2012)

  25. J. Huang and M. Meuwly
    Force Field Refinement from NMR Scalar Couplings
    Chem. Phys., 396, 116 (2012)

  26. U. Gellrich, J. Huang, W. Seiche, M. Keller, M. Meuwly and B. 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)

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

  28. J. Huang and G. Wu
    Dynamical Potential Approach to DCO Highly Excited Vibration
    Chem. Phys. Lett., 439, 231 (2007)

Book Chapters:

  1. J. Huang and M. 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. J. Huang, M. Devereux, F. Hofmann, and M. Meuwly
    Computational Organometallic Chemistry with Force Fields
    Chapter 2 in “Computational Organometallic Chemistry”, Ed: O. Wiest and Y. Wu, Springer, 19-46 (2012)