Jinan Wang

发表

Insight into mechanism of small molecule inhibitors of the MDM2-p53 interaction: molecular dynamics simulation and free energy analysis.

Weiliang Zhu, Jianzhong Chen, Jinan Wang, 2011, Journal of molecular graphics & modelling.

Inhibiting mechanism of small molecule toward the p53‐MDM2 interaction: A molecular dynamic exploration

Weiliang Zhu, Jianzhong Chen, Jinan Wang, 2018, Chemical biology & drug design.

Systems approaches and polypharmacology for drug discovery from herbal medicines: an example using licorice.

Jinan Wang, W. Zhou, Yonghua Wang, 2013, Journal of ethnopharmacology.

The effects of organic solvents on the folding pathway and associated thermodynamics of proteins: a microscopic view

Weiliang Zhu, Jiye Shi, Qiang Shao, 2016, Scientific Reports.

Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding.

Jinan Wang, Y. Miao, 2020, The Journal of chemical physics.

Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding

Jinan Wang, Y. Miao, Yinglong Miao, 2020, bioRxiv.

Exploring Conformational Change of Adenylate Kinase by Replica Exchange Molecular Dynamic Simulation.

Weiliang Zhu, Jiye Shi, Qiang Shao, 2020, Biophysical journal.

Conformation of the Macrocyclic Drug Lorlatinib in Polar and Nonpolar Environments: A MD Simulation and NMR Study

Jiye Shi, Weiliang Zhu, Zhijian Xu, 2019, ACS omega.

Exploring transition pathway and free-energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics.

Jiye Shi, Weiliang Zhu, Zhijian Xu, 2014, The journal of physical chemistry. B.

Exploring molecular mechanism of allosteric inhibitor to relieve drug resistance of multiple mutations in HIV‐1 protease by enhanced conformational sampling

Weiliang Zhu, Jianzhong Chen, Jinan Wang, 2018, Proteins.

Structural requirements of pyrimidine, thienopyridine and ureido thiophene carboxamide-based inhibitors of the checkpoint kinase 1: QSAR, docking, molecular dynamics analysis

Yonghua Wang, Jinan Wang, Yan Li, 2012, Journal of Molecular Modeling.

Unstable, metastable, or stable halogen bonding interaction involving negatively charged donors? A statistical and computational chemistry study.

Weiliang Zhu, Kaixian Chen, Jiye Shi, 2014, The journal of physical chemistry. B.

Exploring binding mechanisms of VEGFR2 with three drugs lenvatinib, sorafenib, and sunitinib by molecular dynamics simulation and free energy calculation

Weiliang Zhu, Jinan Wang, Zhijian Xu, 2019, Chemical biology & drug design.

Systems pharmacology strategies for drug discovery and combination with applications to cardiovascular diseases.

Wei Zhou, Wei Wang, Bohui Li, 2014, Journal of ethnopharmacology.

Ligand Gaussian accelerated molecular dynamics (LiGaMD): Characterization of ligand binding thermodynamics and kinetics

Jinan Wang, Y. Miao, A. Bhattarai, 2020, bioRxiv.

Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations

D. Kozakov, Jinan Wang, Andrey Alekseenko, 2019, bioRxiv.

G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation state

Jinan Wang, Y. Miao, A. Bhattarai, 2019, bioRxiv.

Recent advances in computational studies of GPCR-G protein interactions.

Jinan Wang, Y. Miao, Yinglong Miao, 2019, Advances in protein chemistry and structural biology.

Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors.

Jinan Wang, Y. Miao, 2019, The journal of physical chemistry. B.

Identification of Novel Potential β-N-Acetyl-D-Hexosaminidase Inhibitors by Virtual Screening, Molecular Dynamics Simulation and MM-PBSA Calculations

Yonghua Wang, Jinan Wang, Guohui Li, 2012, International journal of molecular sciences.

Molecular simulation of a series of benzothiazole PI3Kα inhibitors: probing the relationship between structural features, anti-tumor potency and selectivity

Yonghua Wang, Jinan Wang, Zhengtao Xiao, 2012, Journal of Molecular Modeling.

Halogen bonding in differently charged complexes: basic profile, essential interaction terms and intrinsic σ-hole.

Weiliang Zhu, Jiye Shi, Jinan Wang, 2019, Physical chemistry chemical physics : PCCP.

How Do Distance and Solvent Affect Halogen Bonding Involving Negatively Charged Donors?

Weiliang Zhu, Jiye Shi, Qiang Shao, 2016, The journal of physical chemistry. B.

The nature and magnitude of specific halogen bonds between iodo‐perfluorobenzene and heterocyclic systems

Weiliang Zhu, Jinan Wang, Bo Zhang, 2011 .

Systems pharmacology exploration of botanic drug pairs reveals the mechanism for treating different diseases

Jinan Wang, Wei Zhou, Yonghua Wang, 2016, Scientific Reports.

Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation

Weiliang Zhu, Kaixian Chen, Jianzhong Chen, 2015, Scientific Reports.

Velocity-scaling optimized replica exchange molecular dynamics of proteins in a hybrid explicit/implicit solvent.

Weiliang Zhu, Guohui Li, Jinan Wang, 2011, The Journal of chemical physics.

Deciphering molecular mechanism behind conformational change of the São Paolo metallo-β-lactamase 1 by using enhanced sampling

Weiliang Zhu, Jianzhong Chen, Jinan Wang, 2019, Journal of biomolecular structure & dynamics.

System-level multi-target drug discovery from natural products with applications to cardiovascular diseases

Jinan Wang, Yonghua Wang, Chao Huang, 2014, Molecular Diversity.

Improving the accuracy of predicting protein-ligand binding-free energy with semiempirical quantum chemistry charge.

Weiliang Zhu, Jiye Shi, Qiang Shao, 2019, Future medicinal chemistry.

Inhibition of dengue viral infection by diasarone‐I is associated with 2’O methyltransferase of NS5

Kutty Selva Nandakumar, Jinan Wang, Wenyu Wu, 2018, European journal of pharmacology.

On the influence of the mixture of denaturants on protein structure stability: A molecular dynamics study

Weiliang Zhu, Qiang Shao, Jinan Wang, 2014 .

Challenges and frontiers of computational modelling of biomolecular recognition

Jinan Wang, Y. Miao, A. Bhattarai, 2022, QRB Discovery.

AABC_A_247950 1..19

Jinan Wang, Y. Miao, A. Bhattarai, 2022 .

Structures of β1-adrenergic receptor in complex with Gs and ligands of different efficacies

Wei Liu, Jinan Wang, N. Paknejad, 2022, Nature Communications.

Mutation L1196M-induced conformational changes and the drug resistant mechanism of anaplastic lymphoma kinase studied by free energy perturbation and umbrella sampling.

Weiliang Zhu, Jianzhong Chen, Jinan Wang, 2017, Physical chemistry chemical physics : PCCP.

Molecular Mechanism and Energy Basis of Conformational Diversity of Antibody SPE7 Revealed by Molecular Dynamics Simulation and Principal Component Analysis

Weiliang Zhu, Jianzhong Chen, Jinan Wang, 2016, Scientific Reports.

Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics

P. Sexton, A. Christopoulos, A. Tobin, 2023, eLife.

Retrospective Ensemble Docking of Allosteric Modulators in an Adenosine G-Protein-Coupled Receptor

Jinan Wang, Y. Miao, A. Bhattarai, 2020, bioRxiv.

Gaussian Accelerated Molecular Dynamics in OpenMM.

Rommie E. Amaro, Lane W. Votapka, Matthew M Copeland, 2022, The journal of physical chemistry. B.

Trehalose Stabilizing Protein in a Water Replacement Scenario: Insights from Molecular Dynamics Simulation

Weiliang Zhu, Qiang Shao, Jinan Wang, 2019, bioRxiv.

Predicting Biomolecular Binding Kinetics: A Review.

Jinan Wang, Y. Miao, Hung N. Do, 2022, Journal of chemical theory and computation.

Ligand Gaussian accelerated molecular dynamics 2 (LiGaMD2): Improved calculations of ligand binding thermodynamics and kinetics with closed protein pocket

Jinan Wang, Y. Miao, Yinglong Miao, 2022, bioRxiv.

A System-Level Investigation into the Mechanisms of Chinese Traditional Medicine: Compound Danshen Formula for Cardiovascular Disease Treatment

Xue Xu, Hongjun Yang, Haiyu Xu, 2012, PloS one.

TCMSP: a database of systems pharmacology for drug discovery from herbal medicines

Wei Zhou, Peng Li, Ling Yang, 2014, Journal of Cheminformatics.

Small Molecules Targeting the RNA-Binding Protein HuR Inhibit Tumor Growth in Xenografts.

Fei Gao, Jinan Wang, Y. Miao, 2023, Journal of medicinal chemistry.

Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives

Jinan Wang, Y. Miao, A. Bhattarai, 2022, Advances and applications in bioinformatics and chemistry : AABC.

Mechanism of RNA recognition by a Musashi RNA-binding protein

Jinan Wang, Y. Miao, Lan Lan, 2020, bioRxiv.

A Novel Sarsolenane Diterpene as a PTP1B Inhibitor from Hainan Soft Coral Sarcophyton trocheliophorum Marenzeller

Jia Li, Jinan Wang, Yinghuai Zhu, 2017 .

D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics

Weiliang Zhu, Cheng Peng, Kaixian Chen, 2019, J. Chem. Inf. Model..

Gaussian accelerated molecular dynamics: Principles and applications

Jinan Wang, P. Arantes, G. Palermo, 2021, Wiley interdisciplinary reviews. Computational molecular science.

Molecular Simulations and Drug Discovery of Adenosine Receptors

Jinan Wang, Y. Miao, A. Bhattarai, 2022, Molecules.

G‐Protein‐Coupled Receptor–Membrane Interactions Depend on the Receptor Activation State

Yinglong Miao, Apurba Bhattarai, Jinan Wang, 2020, J. Comput. Chem..

Weak-binding molecules are not drugs?—toward a systematic strategy for finding effective weak-binding drugs

Wei Xiao, Chao Huang, Jinan Wang, 2016, Briefings Bioinform..

Recognition of single-stranded nucleic acids by small-molecule splicing modulators

Jinan Wang, M. Reibarkh, J. Douglas, 2021, Nucleic acids research.

Positive allosteric mechanisms of adenosine A1 receptor-mediated analgesia

A. T. Nguyen, P. White, P. Sexton, 2021, Nature.

Identification and Validation of an Aspergillus nidulans Secondary Metabolite Derivative as an Inhibitor of the Musashi-RNA Interaction

J. Karanicolas, Jinan Wang, K. Neufeld, 2020, Cancers.

Q63, a novel DENV2 RdRp non-nucleoside inhibitor, inhibited DENV2 replication and infection.

Kutty Selva Nandakumar, Jinan Wang, Wenyu Wu, 2018, Journal of pharmacological sciences.

Effect of Comb-Type Copolymers on the Non-Isothermal Crystallization Behavior of Paraffin in Methyl Ethyl Ketone (MEK)–Toluene Dewaxing

Lifang Chen, Jinan Wang, Hongyang Li, 2022, Energies.

Large-scale exploration and analysis of drug combinations

Jianxin Chen, Wei Zhou, Peng Li, 2015, Bioinform..

Molecular Mechanism of Binding Selectivity of Inhibitors toward BACE1 and BACE2 Revealed by Multiple Short Molecular Dynamics Simulations and Free Energy Predictions.

Weiliang Zhu, Jianzhong Chen, Jinan Wang, 2019, ACS chemical neuroscience.

Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation.

Weiliang Zhu, Jiye Shi, Qiang Shao, 2015, The Journal of chemical physics.

Mapping central α-helix linker mediated conformational transition pathway of calmodulin via simple computational approach.

Jiye Shi, Xiangke Liao, Weiliang Zhu, 2014, The journal of physical chemistry. B.

Substrate Transport is Mediated not only by P-glycoprotein but also by Lipid Penetration

Weiliang Zhu, Jiye Shi, Qiang Shao, 2019, bioRxiv.

Energetics and structural characterization of the "DFG-flip" conformational transition of B-RAF kinase: a SITS molecular dynamics study.

Weiliang Zhu, Jiye Shi, Qiang Shao, 2017, Physical chemistry chemical physics : PCCP.

Dynamics revelation of conformational changes and binding modes of heat shock protein 90 induced by inhibitor associations

Weiliang Zhu, Jianzhong Chen, Jinan Wang, 2018, RSC advances.

Structural basis for DNA recognition by STAT6

G. Cheng, Qiang Shao, L. Hung, 2016, Proceedings of the National Academy of Sciences.

Mechanism of Tripeptide Trimming of Amyloid β-Peptide 49 by γ-Secretase.

M. Wolfe, Jinan Wang, Y. Miao, 2022, Journal of the American Chemical Society.

Mechanism of Tripeptide Trimming by γ-Secretase

M. Wolfe, Jinan Wang, Y. Miao, 2021, bioRxiv.

Increasing the Sampling Efficiency of Protein Conformational Change by Combining a Modified Replica Exchange Molecular Dynamics and Normal Mode Analysis.

Weiliang Zhu, Jinan Wang, Zhijian Xu, 2020, Journal of chemical theory and computation.

Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors

Jinan Wang, Y. Miao, Hung N. Do, 2023, bioRxiv.

Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors

Jinan Wang, Y. Miao, Hung N. Do, 2023, Research square.

Binding competition to the POPG lipid bilayer of Ca2+, Mg2+, Na+, and K+ in different ion mixtures and biological implication.

Hualiang Jiang, Jinan Wang, Huaiyu Yang, 2013, The journal of physical chemistry. B.

Discovery of potent and selective Bcl-2 inhibitors with acyl sulfonamide skeleton.

Jinan Wang, W. Shi, Hongjian Xu, 2021, Bioorganic & medicinal chemistry.

Estimation of acute oral toxicity in rat using local lazy learning

Xiaomin Luo, Weiliang Zhu, Jing Lu, 2014, Journal of Cheminformatics.

Computer-aided GPCR drug discovery

Yinglong Miao, Jinan Wang, Apurba Bhattarai, 2020 .

Specific Engineered G Protein Coupling to Histamine Receptors Revealed from Cellular Assay Experiments and Accelerated Molecular Dynamics Simulations

Christian A. Söldner, A. Strasser, Jinan Wang, 2021, International journal of molecular sciences.

Stability and Characteristics of the Halogen Bonding Interaction in an Anion-Anion Complex: A Computational Chemistry Study.

Jiye Shi, Yang Yang, Zhijian Xu, 2016, The journal of physical chemistry. B.

A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings

Weiliang Zhu, Guohui Li, Jinan Wang, 2013, Journal of Computer-Aided Molecular Design.

The stabilization effect of dielectric constant and acidic amino acids on arginine-arginine (Arg-Arg) pairings: database survey and computational studies.

Weiliang Zhu, Qiang Shao, Jinan Wang, 2013, The journal of physical chemistry. B.

Binding Modes of Three Inhibitors 8CA, F8A and I4A to A-FABP Studied Based on Molecular Dynamics Simulation

Weiliang Zhu, Jianzhong Chen, Jinan Wang, 2014, PloS one.

Collaborative Behavior of Urea and KI in Denaturing Protein Native Structure

Weiliang Zhu, Qiang Shao, Jinan Wang, 2019, bioRxiv.

Like-Charge Guanidinium Pairing between Ligand and Receptor: An Unusual Interaction for Drug Discovery and Design?

Jiye Shi, Yang Yang, Shujin Li, 2015, The journal of physical chemistry. B.

Protein-Protein Interaction-Gaussian Accelerated Molecular Dynamics (PPI-GaMD): Characterization of Protein Binding Thermodynamics and Kinetics.

Jinan Wang, Y. Miao, 2022, Journal of chemical theory and computation.

Protein-protein interaction-Gaussian accelerated molecular dynamics (PPI-GaMD): Characterization of protein binding thermodynamics and kinetics

Jinan Wang, Y. Miao, Yinglong Miao, 2021, bioRxiv.

Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations

D. Kozakov, Jinan Wang, Andrey Alekseenko, 2019, Frontiers in molecular biosciences.

Structural insights into HIV-1 protease flap opening processes and key intermediates

Weiliang Zhu, Jiye Shi, Qiang Shao, 2017 .

Ammonium Transport Proteins with Changes in One of the Conserved Pore Histidines Have Different Performance in Ammonia and Methylamine Conduction

Weiliang Zhu, Mike Merrick, Qiang Shao, 2013, PloS one.

Effects of drug-resistant mutations on the dynamic properties of HIV-1 protease and inhibition by Amprenavir and Darunavir

Weiliang Zhu, Jiye Shi, Qiang Shao, 2015, Scientific Reports.

The universality of β-hairpin misfolding indicated by molecular dynamics simulations.

Weiliang Zhu, Jiye Shi, Qiang Shao, 2013, The Journal of chemical physics.

Zinc ion-induced conformational changes in new Delphi metallo-β-lactamase 1 probed by molecular dynamics simulations and umbrella sampling.

Weiliang Zhu, Jianzhong Chen, Jinan Wang, 2017, Physical chemistry chemical physics : PCCP.

A comparative study of trypsin specificity based on QM/MM molecular dynamics simulation and QM/MM GBSA calculation

Weiliang Zhu, Qinggang Zhang, Jianzhong Chen, 2015, Journal of biomolecular structure & dynamics.

Accurate prediction of relative binding affinities of a series of HIV‐1 protease inhibitors using semi‐empirical quantum mechanical charge

Weiliang Zhu, Cheng Peng, Zhijian Xu, 2020, J. Comput. Chem..

Insight into the binding mode and the structural features of the pyrimidine derivatives as human A2A adenosine receptor antagonists

Xia Wang, Ling Yang, Guohui Li, 2014, Biosyst..

Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors Revealed by Accelerated Molecular Simulations

Jinan Wang, Y. Miao, Yinglong Miao, 2019, bioRxiv.

Structural basis of agonist specificity of α1A-adrenergic receptor

Jinan Wang, Xin-Yun Huang, Y. Miao, 2023, Nature communications.

Thermodynamics calculation of protein–ligand interactions by QM/MM polarizable charge parameters

Jiye Shi, Weiliang Zhu, Benjamin P. Cossins, 2016, Journal of biomolecular structure & dynamics.

GLOW: A Workflow Integrating Gaussian-Accelerated Molecular Dynamics and Deep Learning for Free Energy Profiling.

Jinan Wang, Y. Miao, A. Bhattarai, 2022, Journal of chemical theory and computation.

Systems approaches and polypharmacology for drug discovery from herbal medicines: an example using licorice.

Jinan Wang, W. Zhou, Yonghua Wang, 2013, Journal of ethnopharmacology.

Unstable, metastable, or stable halogen bonding interaction involving negatively charged donors? A statistical and computational chemistry study.

Weiliang Zhu, Kaixian Chen, Jiye Shi, 2014, The journal of physical chemistry. B.

Zinc ion-induced conformational changes in new Delphi metallo-β-lactamase 1 probed by molecular dynamics simulations and umbrella sampling.

Weiliang Zhu, Jianzhong Chen, Jinan Wang, 2017, Physical chemistry chemical physics : PCCP.

Exploring transition pathway and free-energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics.

Benjamin P. Cossins, Weiliang Zhu, Kaixian Chen, 2014, The journal of physical chemistry. B.