Jing Huang

发表

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

B. L. de Groot, H. Grubmüller, M. Feig, 2016, Nature Methods.

Force field development and simulations of intrinsically disordered proteins.

Alexander D. MacKerell, Jing Huang, 2018, Current opinion in structural biology.

Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model

Alexander D. MacKerell, Pedro E. M. Lopes, B. Roux, 2014, The journal of physical chemistry letters.

CHARMM36: An Improved Force Field for Folded and Intrinsically Disordered Proteins

Alexander D. MacKerell, Helmut Grubmüller, Jing Huang, 2017 .

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

Alexander D. MacKerell, Benoît Roux, Jing Huang, 2016, Chemical reviews.

Turning Defense into Offense: Defensin Mimetics as Novel Antibiotics Targeting Lipid II

Alexander D. MacKerell, A. Bonvin, Jing Huang, 2013, PLoS pathogens.

Structure–activity exploration of a small-molecule Lipid II inhibitor

Alexander D. MacKerell, Jing Huang, S. Fletcher, 2015, Drug design, development and therapy.

Enhanced Conformational Sampling Using Replica Exchange with Concurrent Solute Scaling and Hamiltonian Biasing Realized in One Dimension

Alexander D. MacKerell, Jing Huang, Mingjun Yang, 2015, Journal of chemical theory and computation.

VBEFP/PCM: a QM/MM/PCM approach for valence-bond method and its application for the vertical excitations of formaldehyde and acetone in aqueous solution

Wei Wu, Jing Huang, Peifeng Su, 2014, Science China Chemistry.

Conformational Heterogeneity of the HIV Envelope Glycan Shield

Lai-Xi Wang, Jing Huang, A. MacKerell, 2017, Scientific Reports.

On the Transferability of CHARMM36m Protein Force Field with LJ-PME: Hydrogen Bonding Dynamics under Elevated Pressures

Jing Huang, You Xu, 2021 .

Methylguanidinium at the Air/Water Interface: A Simulation Study with the Drude Polarizable Force Field.

Jing Huang, Jian Zhu, 2020, The journal of physical chemistry. B.

Conformational Heterogeneity of Intracellular Loop 3 of the μ-opioid G-protein Coupled Receptor.

Alexander D. MacKerell, S. K. Lakkaraju, Jing Huang, 2016, The journal of physical chemistry. B.

Structural Achievability of an NH–π Interaction between Gln and Phe in a Crystal Structure of a Collagen-like Peptide

Jing Huang, You Xu, J. Lan, 2022, Biomolecules.

Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation.

Alexander D. MacKerell, Jing Huang, Nien-Hui Ge, 2016, The journal of physical chemistry. B.

CHARMM36 all‐atom additive protein force field: Validation based on comparison to NMR data

Jing Huang, Alexander D. MacKerell, Jing Huang, 2013, J. Comput. Chem..

Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations.

Andrew C Simmonett, Bernard R Brooks, Jing Huang, 2018, Journal of chemical theory and computation.

Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks

Alexander D. MacKerell, Jing Huang, Justin A. Lemkul, 2018, J. Comput. Chem..

Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.

Alexander D. MacKerell, B. Roux, Jing Huang, 2020, Journal of chemical theory and computation.

Force Field for Peptides and Proteins based on the Classical Drude Oscillator.

Alexander D. MacKerell, Pedro E. M. Lopes, B. Roux, 2013, Journal of chemical theory and computation.

TITAN: A Code for Modeling and Generating Electric Fields—Features and Applications to Enzymatic Reactivity

Sason Shaik, Jing Huang, David Danovich, 2020, J. Comput. Chem..

Induced Dipole–Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides

Alexander D. MacKerell, Justin A. Lemkul, Jing Huang, 2015, Journal of Physical Chemistry B.

DIRECT‐ID: An automated method to identify and quantify conformational variations—application to β2‐adrenergic GPCR

Alexander D. MacKerell, Jing Huang, Sirish Kaushik Lakkaraju, 2016, J. Comput. Chem..

A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

Alexander D. MacKerell, Bernard R Brooks, Walter Thiel, 2018, Molecules.

Mapping the Drude polarizable force field onto a multipole and induced dipole model.

Alexander D. MacKerell, Andrew C Simmonett, Bernard R Brooks, 2017, The Journal of chemical physics.

An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge

Bernard R. Brooks, Samarjeet Prasad, Jing Huang, 2018, Journal of Computer-Aided Molecular Design.

Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

Chaok Seok, Bernard R. Brooks, Juyong Lee, 2016, Journal of Computer-Aided Molecular Design.

Absolute binding free energies for octa-acids and guests in SAMPL5

Chaok Seok, Bernard R. Brooks, Juyong Lee, 2016, Journal of Computer-Aided Molecular Design.

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Alexander D. MacKerell, Andrew C Simmonett, Bernard R Brooks, 2017, Journal of chemical theory and computation.

Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide.

Alexander D. MacKerell, Jing Huang, 2014, Biophysical journal.

Conformational Heterogeneity of the HIV Envelope Glycan Shield

Lai-Xi Wang, Jing Huang, A. MacKerell, 2017, Scientific Reports.

Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects.

Andrew C Simmonett, Bernard R Brooks, Jing Huang, 2019, Journal of chemical theory and computation.

Towards Development of Small Molecule Lipid II Inhibitors as Novel Antibiotics

Alexander D. MacKerell, Jing Huang, S. Fletcher, 2016, PloS one.

Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide.

Alexander D. MacKerell, Jing Huang, 2014, Biophysical journal.

DIRECT‐ID: An automated method to identify and quantify conformational variations—application to β2‐adrenergic GPCR

Alexander D. MacKerell, Justin A. Lemkul, S. K. Lakkaraju, 2016, J. Comput. Chem..

Structure–activity exploration of a small-molecule Lipid II inhibitor

Alexander D. MacKerell, Jing Huang, S. Fletcher, 2015, Drug design, development and therapy.

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

Bernard R. Brooks, Juyong Lee, Walter Thiel, 2016, Journal of Computer-Aided Molecular Design.

Mapping the Drude polarizable force field onto a multipole and induced dipole model.

Alexander D. MacKerell, Andrew C. Simmonett, Frank C. Pickard, 2017, Journal of Chemical Physics.

Enhanced Conformational Sampling Using Replica Exchange with Concurrent Solute Scaling and Hamiltonian Biasing Realized in One Dimension

Alexander D. MacKerell, Jing Huang, Mingjun Yang, 2015, Journal of chemical theory and computation.