Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations

Finding chemical drugs for genetic diseases

(2014) Hui-Yong Sun et al.   DRUG DISCOVERY TODAY

Unbinding Pathways of VEGFR2 Inhibitors Revealed by Steered Molecular Dynamics

(2014) Anna Maria Capelli et al.   Journal of Chemical Information and Modeling

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

P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape

(2014) Huiyong Sun et al.   PLoS Computational Biology

The Dynamic Process of β2-Adrenergic Receptor Activation

(2013) Rie Nygaard et al.   CELL

Structural and Energetic Analyses of SNPs in Drug Targets and Implications for Drug Therapy

(2013) Hui-Yong Sun et al.   Journal of Chemical Information and Modeling

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

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

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

Exploring Transition Pathway and Free-Energy Profile of Large-Scale Protein Conformational Change by Combining Normal Mode Analysis and Umbrella Sampling Molecular Dynamics

(2013) Jinan Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Free energy landscape for the binding process of Huperzine A to acetylcholinesterase

(2013) Fang Bai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants R155K, A156V and D168A to TMC435

(2011) Weiwei Xue et al.   ANTIVIRAL RESEARCH

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

Use of Umbrella Sampling to Calculate the Entrance/Exit Pathway for Z-Pro-Prolinal Inhibitor in Prolyl Oligopeptidase

(2011) Jean-François St-Pierre et al.   Journal of Chemical Theory and Computation

Activation mechanism of the  2-adrenergic receptor

(2011) R. O. Dror et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

Insights into MAPK p38α DFG flip mechanism by accelerated molecular dynamics

(2010) Federico Filomia et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Sequence, Structure, and Active Site Analyses of p38 MAP Kinase: Exploiting DFG-out Conformation as a Strategy to Design New Type II Leads

(2010) Preethi Badrinarayan et al.   Journal of Chemical Information and Modeling

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

Quo Vadis, Virtual Screening? A Comprehensive Survey of Prospective Applications

(2010) Peter Ripphausen et al.   JOURNAL OF MEDICINAL CHEMISTRY

Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force

(2009) Slimane Doudou et al.   Journal of Chemical Theory and Computation

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

(2009) Jérome Hénin et al.   Journal of Chemical Theory and Computation

Steered Molecular Dynamics Simulations Reveal the Likelier Dissociation Pathway of Imatinib from Its Targeting Kinases c-Kit and Abl

(2009) Li-Jun Yang et al.   PLoS One

Adaptive biasing force method for scalar and vector free energy calculations

(2008) Eric Darve et al.   JOURNAL OF CHEMICAL PHYSICS

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS