Insight into the selective mechanism of phosphoinositide 3-kinase γ with benzothiazole and thiazolopiperidine γ-specific inhibitors by in silico approaches

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches

(2018) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes

(2018) Fu Chen et al.   RNA

Combating Drug-Resistant Mutants of Anaplastic Lymphoma Kinase with Potent and Selective Type-I1/2 Inhibitors by Stabilizing Unique DFG-Shifted Loop Conformation

(2017) Peichen Pan et al.   ACS Central Science

Theoretical studies on the selective mechanisms of GSK3β and CDK2 by molecular dynamics simulations and free energy calculations

(2016) Sufang Zhao et al.   Chemical Biology & Drug Design

Virtual screening of small molecules databases for discovery of novel PARP-1 inhibitors: combination of in silico and in vitro studies

(2016) Ramin Ekhteiari Salmas et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

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

Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power

(2016) Zhe Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Discovery of selective phosphatidylinositol 3-kinase inhibitors to treat hematological malignancies

(2015) Jingyu Zhu et al.   DRUG DISCOVERY TODAY

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder et al.   Journal of Chemical Theory and Computation

Discovery of Highly Isoform Selective Thiazolopiperidine Inhibitors of Phosphoinositide 3-Kinase γ

(2015) Philip N. Collier et al.   JOURNAL OF MEDICINAL CHEMISTRY

Targeting the Phosphatidylinositol 3-Kinase/AKT Pathway for the Treatment of Multiple Myeloma

(2014) J. Zhu et al.   CURRENT MEDICINAL CHEMISTRY

Structural Basis for Isoform Selectivity in a Class of Benzothiazole Inhibitors of Phosphoinositide 3-Kinase γ

(2014) Philip N. Collier 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

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

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

Exploring the Molecular Mechanism of Cross-Resistance to HIV-1 Integrase Strand Transfer Inhibitors by Molecular Dynamics Simulation and Residue Interaction Network Analysis

(2012) Weiwei Xue et al.   Journal of Chemical Information and Modeling

Blockade of Phosphatidylinositol 3-Kinase (PI3K)δ or PI3Kγ Reduces IL-17 and Ameliorates Imiquimod-Induced Psoriasis-like Dermatitis

(2012) Anne Roller et al.   JOURNAL OF IMMUNOLOGY

Understanding microscopic binding of macrophage migration inhibitory factor with phenolic hydrazones by molecular docking, molecular dynamics simulations and free energy calculations

(2012) Lei Xu et al.   Molecular BioSystems

Molecular dynamics and free energy studies on Aurora kinase A and its mutant bound with MLN8054: insight into molecular mechanism of subtype selectivity

(2012) Ying Yang et al.   Molecular BioSystems

Understanding the effect of drug-resistant mutations of HIV-1 intasome on raltegravir action through molecular modeling study

(2012) Weiwei Xue et al.   Molecular BioSystems

Understanding the structural and energetic basis of inhibitor and substrate bound to the full-length NS3/4A: insights from molecular dynamics simulation, binding free energy calculation and network analysis

(2012) Weiwei Xue et al.   Molecular BioSystems

A selective inhibitor reveals PI3Kγ dependence of TH17 cell differentiation

(2012) Giovanna Bergamini et al.   Nature Chemical Biology

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

(2011) Tingjun Hou et al.   BIOINFORMATICS

Molecular Dynamics Simulation and Free Energy Calculation Studies of the Binding Mechanism of Allosteric Inhibitors with p38α MAP Kinase

(2011) Ying Yang et al.   Journal of Chemical Information and Modeling

CAL-101, a p110  selective phosphatidylinositol-3-kinase inhibitor for the treatment of B-cell malignancies, inhibits PI3K signaling and cellular viability

(2010) B. J. Lannutti et al.   BLOOD

In SilicoIdentification of the Potential Drug Resistance Sites over 2009 Influenza A (H1N1) Virus Neuraminidase

(2010) Huanxiang Liu et al.   MOLECULAR PHARMACEUTICS

The emerging mechanisms of isoform-specific PI3K signalling

(2010) Bart Vanhaesebroeck et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance

(2010) J. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of Domain–Peptide Interaction Interface: A Case Study on the Amphiphysin-1 SH3 Domain

(2008) Tingjun Hou et al.   JOURNAL OF MOLECULAR BIOLOGY