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Jing Huang - Publications

Affiliations: 
University of Basel, Basel, Basel-Stadt, Switzerland 
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25 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Hwang W, Austin SL, Blondel A, Boittier ED, Boresch S, Buck M, Buckner J, Caflisch A, Chang HT, Cheng X, Choi YK, Chu JW, Crowley MF, Cui Q, Damjanovic A, ... ... Huang J, et al. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. The Journal of Physical Chemistry. B. PMID 39303207 DOI: 10.1021/acs.jpcb.4c04100  0.503
2020 Lin FY, Huang J, Pandey P, Rupakheti C, Li J, Roux B, MacKerell AD. Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field. Journal of Chemical Theory and Computation. PMID 32282198 DOI: 10.1021/Acs.Jctc.0C00057  0.338
2018 König G, Pickard FC, Huang J, Thiel W, MacKerell AD, Brooks BR, York DM. A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes. Molecules (Basel, Switzerland). 23. PMID 30347691 DOI: 10.3390/Molecules23102695  0.352
2018 Huang J, Lemkul JA, Eastman PK, MacKerell AD. Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks. Journal of Computational Chemistry. PMID 29727037 DOI: 10.1002/Jcc.25339  0.329
2017 Leonard AN, Simmonett AC, Pickard FC, Huang J, Venable RM, Klauda JB, Brooks BR, Pastor RW. Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions using Alkane Simulations. Journal of Chemical Theory and Computation. PMID 29268012 DOI: 10.1021/Acs.Jctc.7B00948  0.333
2017 Huang J, Simmonett AC, Pickard FC, MacKerell AD, Brooks BR. Mapping the Drude polarizable force field onto a multipole and induced dipole model. The Journal of Chemical Physics. 147: 161702. PMID 29096511 DOI: 10.1063/1.4984113  0.306
2017 Huang J, Mei Y, Koenig G, Simmonett AC, Pickard FC, Wu Q, Wang LP, MacKerell AD, Brooks BR, Shao Y. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical (QM/MM) Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches. Journal of Chemical Theory and Computation. PMID 28081366 DOI: 10.1021/Acs.Jctc.6B01125  0.3
2016 Lee J, Tofoleanu F, Pickard FC, König G, Huang J, Damjanović A, Baek M, Seok C, Brooks BR. Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge. Journal of Computer-Aided Molecular Design. PMID 27677749 DOI: 10.1007/S10822-016-9968-2  0.342
2016 König G, Pickard FC, Huang J, Simmonett AC, Tofoleanu F, Lee J, Dral PO, Prasad S, Jones M, Shao Y, Thiel W, Brooks BR. 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. Journal of Computer-Aided Molecular Design. PMID 27577746 DOI: 10.1007/S10822-016-9936-X  0.341
2016 Feng Y, Huang J, Kim S, Shim JH, MacKerell AD, Ge NH. Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation. The Journal of Physical Chemistry. B. PMID 27299801 DOI: 10.1021/Acs.Jpcb.6B02608  0.312
2016 Lemkul JA, Huang J, Roux B, MacKerell AD. An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications. Chemical Reviews. PMID 26815602 DOI: 10.1021/Acs.Chemrev.5B00505  0.375
2015 Lemkul JA, Huang J, MacKerell AD. Induced Dipole-Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides. The Journal of Physical Chemistry. B. PMID 26629591 DOI: 10.1021/Acs.Jpcb.5B09978  0.324
2015 Lakkaraju SK, Lemkul JA, Huang J, MacKerell AD. DIRECT-ID: An automated method to identify and quantify conformational variations-application to β2 -adrenergic GPCR. Journal of Computational Chemistry. PMID 26558323 DOI: 10.1002/Jcc.24231  0.343
2015 Howard DL, Kjaergaard HG, Huang J, Meuwly M. Infrared and Near-Infrared Spectroscopy of Acetylacetone and Hexafluoroacetylacetone. The Journal of Physical Chemistry. A. PMID 25894207 DOI: 10.1021/Acs.Jpca.5B01863  0.528
2015 Huang J, MacKerell AD. Cooperative Helix Formation in the (AAQAA)3 Peptide Obtained with the Drude Polarizable Force Field Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.2839  0.318
2014 Huang J, Lopes PE, Roux B, MacKerell AD. Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model. The Journal of Physical Chemistry Letters. 5: 3144-3150. PMID 25247054 DOI: 10.1021/Jz501315H  0.325
2014 Huang J, Buchowiecki M, Nagy T, Vaní?ek J, Meuwly M. Kinetic isotope effect in malonaldehyde determined from path integral Monte Carlo simulations. Physical Chemistry Chemical Physics : Pccp. 16: 204-11. PMID 24233185 DOI: 10.1039/C3Cp53698J  0.593
2014 Lopes PE, Huang J, Shim J, Luo Y, Li H, Savelyev A, Patel D, He X, Roux B, MacKerell AD. Development of a Polarizable Force Field for Macromolecules Based on the Classical Drude Oscillator Biophysical Journal. 106: 43a. DOI: 10.1016/J.Bpj.2013.11.318  0.313
2013 Lopes PE, Huang J, Shim J, Luo Y, Li H, Roux B, Mackerell AD. Force Field for Peptides and Proteins based on the Classical Drude Oscillator. Journal of Chemical Theory and Computation. 9: 5430-5449. PMID 24459460 DOI: 10.1021/Ct400781B  0.32
2013 Huang J, MacKerell AD. CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. Journal of Computational Chemistry. 34: 2135-45. PMID 23832629 DOI: 10.1002/Jcc.23354  0.331
2012 Huang J, Häussinger D, Gellrich U, Seiche W, Breit B, Meuwly M. Hydrogen-bond and solvent dynamics in transition metal complexes: A combined simulation and NMR-investigation Journal of Physical Chemistry B. 116: 14406-14415. PMID 23127212 DOI: 10.1021/Jp309412R  0.541
2012 Cazade PA, Huang J, Yosa J, Szymczak JJ, Meuwly M. Atomistic simulations of reactive processes in the gas- and condensed-phase International Reviews in Physical Chemistry. 31: 235-264. DOI: 10.1080/0144235X.2012.694694  0.514
2012 Huang J, Meuwly M. Force field refinement from NMR scalar couplings Chemical Physics. 396: 116-123. DOI: 10.1016/J.Chemphys.2011.09.016  0.527
2011 Gellrich U, Huang J, Seiche W, Keller M, Meuwly M, Breit B. Ligand self-assembling through complementary hydrogen-bonding in the coordination sphere of a transition metal center: the 6-diphenylphosphanylpyridin-2(1H)-one system. Journal of the American Chemical Society. 133: 964-75. PMID 21142007 DOI: 10.1021/Ja108639E  0.503
2010 Huang J, Meuwly M. Explicit Hydrogen-Bond Potentials and Their Application to NMR Scalar Couplings in Proteins. Journal of Chemical Theory and Computation. 6: 467-76. PMID 26617302 DOI: 10.1021/Ct9005695  0.532
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