Insight into tetrodotoxin blockade and resistance mechanisms of Nav 1.2 sodium channel by theoretical approaches

Prediction of luciferase inhibitors by the high-performance MIEC-GBDT approach based on interaction energetic patterns

(2017) Fu Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Directly Binding Rather than Induced-Fit Dominated Binding Affinity Difference in (S)- and (R)-Crizotinib Bound MTH1

(2016) Huiyong Sun et al.   Journal of Chemical Theory and Computation

Identification of the inhibitory mechanism of FDA approved selective serotonin reuptake inhibitors: an insight from molecular dynamics simulation study

(2016) Weiwei Xue et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking

(2016) Fu Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Constructing and Validating High-Performance MIEC-SVM Models in Virtual Screening for Kinases: A Better Way for Actives Discovery

(2016) Huiyong Sun et al.   Scientific Reports

Molecular Dynamics Simulations of Ternary Complexes: Comparisons of LEAFY Protein Binding to Different DNA Motifs

(2015) Hua Wan et al.   Journal of Chemical Information and Modeling

Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease

(2015) Nan Li et al.   Journal of Chemical Information and Modeling

Voltage-Gated Sodium Channels: Structure, Function, Pharmacology, and Clinical Indications

(2015) Manuel de Lera Ruiz et al.   JOURNAL OF MEDICINAL CHEMISTRY

Exploring the binding mechanisms of MIF to CXCR2 using theoretical approaches

(2015) Lei Xu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Importance of protein flexibility in ranking inhibitor affinities: modeling the binding mechanisms of piperidine carboxamides as Type I1/2 ALK inhibitors

(2015) Xiaotian Kong et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The competitive binding between inhibitors and substrates of HCV NS3/4A protease: A general mechanism of drug resistance

(2014) Yan Guan et al.   ANTIVIRAL RESEARCH

Mechanism of tetrodotoxin block and resistance in sodium channels

(2014) Rong Chen et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Molecular modeling study on the dynamical structural features of human smoothened receptor and binding mechanism of antagonist LY2940680 by metadynamics simulation and free energy calculation

(2014) Qifeng Bai et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Modeling, Molecular Dynamics Simulation, and Mutation Validation for Structure of Cannabinoid Receptor 2 Based on Known Crystal Structures of GPCRs

(2014) Zhiwei Feng et al.   Journal of Chemical Information and Modeling

Discovery of Novel Inhibitors Targeting the Macrophage Migration Inhibitory Factor via Structure-Based Virtual Screening and Bioassays

(2014) Lei Xu et al.   JOURNAL OF MEDICINAL CHEMISTRY

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Insights into susceptibility of antiviral drugs against the E119G mutant of 2009 influenza A (H1N1) neuraminidase by molecular dynamics simulations and free energy calculations

(2013) Peichen Pan et al.   ANTIVIRAL RESEARCH

Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches

(2013) Huiyong Sun et al.   Journal of Chemical Information and Modeling

Ligand- and Structure-Based Virtual Screening for Clathrodin-Derived Human Voltage-Gated Sodium Channel Modulators

(2013) Tihomir Tomašić et al.   Journal of Chemical Information and Modeling

Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches

(2013) Peichen Pan et al.   Journal of Chemical Information and Modeling

Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models

(2013) Lei Xu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural basis of the interactions between CXCR4 and CXCL12/SDF-1 revealed by theoretical approaches

(2013) Lei Xu et al.   Molecular BioSystems

Corrigendum: Advances in Targeting Voltage-Gated Sodium Channels with Small Molecules

(2012) Antonio Nardi et al.   ChemMedChem

Theoretical Studies on the Susceptibility of Oseltamivir against Variants of 2009 A/H1N1 Influenza Neuraminidase

(2012) Lin Li et al.   Journal of Chemical Information and Modeling

Concerted Movement in pH-Dependent Gating of FocA from Molecular Dynamics Simulations

(2012) Zhiwei Feng et al.   Journal of Chemical Information and Modeling

Ion Channels as Therapeutic Targets: A Drug Discovery Perspective

(2012) Sharan K. Bagal et al.   JOURNAL OF MEDICINAL CHEMISTRY

Characterization of Domain–Peptide Interaction Interface: Prediction of SH3 Domain-Mediated Protein–Protein Interaction Network in Yeast by Generic Structure-Based Models

(2012) Tingjun Hou et al.   JOURNAL OF PROTEOME RESEARCH

Discovery and optimization of triazine derivatives as ROCK1 inhibitors: molecular docking, molecular dynamics simulations and free energy calculations

(2012) Mingyun Shen et al.   Molecular BioSystems

Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy

(2011) Tingjun Hou et al.   BIOINFORMATICS

The crystal structure of a voltage-gated sodium channel

(2011) Jian Payandeh et al.   NATURE

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

(2010) Tingjun Hou et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Lipidbook: A Public Repository for Force-Field Parameters Used in Membrane Simulations

(2010) Jan Domański et al.   JOURNAL OF MEMBRANE BIOLOGY

The Tetrodotoxin Binding Site Is within the Outer Vestibule of the Sodium Channel

(2010) Harry A. Fozzard et al.   Marine Drugs

Voltage-gated sodium channels in pain states: Role in pathophysiology and targets for treatment

(2008) Sulayman D. Dib-Hajj et al.   BRAIN RESEARCH REVIEWS