IBBR Publications

Found 21 results
Filters: Author is Huang, Jing  [Clear All Filters]
2020
Lin F-Y, Huang J, Pandey P, Rupakheti C, Li J, Roux B, Mackerell AD. Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field. J Chem Theory Comput. 2020 .
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. 2018 ;23(10).
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. J Comput Chem. 2018 .
2017
Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmüller H, Mackerell AD. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat Methods. 2017 ;14(1):71-73.
Yang M, Huang J, Simon R, Wang L-X, Mackerell AD. Conformational Heterogeneity of the HIV Envelope Glycan Shield. Sci Rep. 2017 ;7(1):4435.
Huang J, Mei Y, König G, Simmonett AC, Pickard FC, Wu Q, Wang L-P, Mackerell AD, Brooks BR, Shao Y. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches. J Chem Theory Comput. 2017 ;13(2):679-695.
Huang J, Mackerell AD. Force field development and simulations of intrinsically disordered proteins. Curr Opin Struct Biol. 2017 ;48:40-48.
Huang J, Simmonett AC, Pickard FC, Mackerell AD, Brooks BR. Mapping the Drude polarizable force field onto a multipole and induced dipole model. J Chem Phys. 2017 ;147(16):161702.
2016
Huang J, Lakkaraju SKaushik, Coop A, Mackerell AD. Conformational Heterogeneity of Intracellular Loop 3 of the μ-opioid G-protein Coupled Receptor. J Phys Chem B. 2016 ;120(46):11897-11904.
Lakkaraju SKaushik, Lemkul JA, Huang J, Mackerell AD. DIRECT-ID: An automated method to identify and quantify conformational variations--application to β2 -adrenergic GPCR. J Comput Chem. 2016 ;37(4):416-25.
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. Chem Rev. 2016 ;116(9):4983-5013.
Feng Y, Huang J, Kim S, Shim JHyun, Mackerell AD, Ge N-H. Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation. J Phys Chem B. 2016 ;120(24):5325-39.
Chauhan J, Cardinale S, Fang L, Huang J, Kwasny SM, M Pennington R, Basi K, diTargiani R, Capacio BR, Mackerell AD, et al. Towards Development of Small Molecule Lipid II Inhibitors as Novel Antibiotics. PLoS One. 2016 ;11(10):e0164515.
2015
Yang M, Huang J, Mackerell AD. Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension. J Chem Theory Comput. 2015 ;11(6):2855-67.
Lemkul JA, Huang J, Mackerell AD. Induced Dipole-Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides. J Phys Chem B. 2015 ;119(51):15574-82.
Fletcher S, Yu W, Huang J, Kwasny SM, Chauhan J, Opperman TJ, Mackerell AD, de Leeuw EPH. Structure-activity exploration of a small-molecule Lipid II inhibitor. Drug Des Devel Ther. 2015 ;9:2383-94.
2014
Huang J, Mackerell AD. Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide. Biophys J. 2014 ;107(4):991-7.
Huang J, Lopes PEM, Roux B, Mackerell AD. Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model. J Phys Chem Lett. 2014 ;5(18):3144-3150.
2013
Huang J, Mackerell AD. CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J Comput Chem. 2013 ;34(25):2135-45.
Lopes PEM, Huang J, Shim J, Luo Y, Li H, Roux B, Mackerell AD. Force Field for Peptides and Proteins based on the Classical Drude Oscillator. J Chem Theory Comput. 2013 ;9(12):5430-5449.
Varney KM, Bonvin AMJJ, Pazgier M, Malin J, Yu W, Ateh E, Oashi T, Lu W, Huang J, de Buin MDiepeveen-, et al. Turning defense into offense: defensin mimetics as novel antibiotics targeting lipid II. PLoS Pathog. 2013 ;9(11):e1003732.