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

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

(2015) Jianzhong Chen et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Computational discovery and experimental verification of tyrosine kinase inhibitor pazopanib for the reversal of memory and cognitive deficits in rat model neurodegeneration

(2015) Yongliang Yang et al.   Chemical Science

Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain

(2014) Grzegorz Popowicz et al.   CELL CYCLE

CH–π hydrogen bonds in biological macromolecules

(2014) Motohiro Nishio et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2014) Jianzhong Chen et al.   PLoS One

Insight into the interaction mechanism of inhibitors P4 and WK23 with MDM2 based on molecular dynamics simulation and different free energy methods

(2014) Shuhua Shi et al.   Computational and Theoretical Chemistry

Investigating the Impact of Asp181 Point Mutations on Interactions between PTP1B and Phosphotyrosine Substrate

(2014) Mengyuan Liu et al.   Scientific Reports

Revealing Origin of Decrease in Potency of Darunavir and Amprenavir against HIV-2 relative to HIV-1 Protease by Molecular Dynamics Simulations

(2014) Jianzhong Chen et al.   Scientific Reports

Ligand selectivity of estrogen receptors by a molecular dynamics study

(2013) Guodong Hu et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Interchain hydrophobic clustering promotes rigidity in HIV-1 protease flap dynamics: new insights from Molecular Dynamics

(2013) Biswa Ranjan Meher et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

A New Quantum Calibrated Force Field for Zinc–Protein Complex

(2013) Tong Zhu et al.   Journal of Chemical Theory and Computation

The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect

(2013) Juan Zeng et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2013) Jianzhong Chen et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Structural and magnetic properties of Sr2FeMoO6 film prepared by electrophoresis technique

(2013) Q. Zhang et al.   JOURNAL OF MAGNETISM AND MAGNETIC MATERIALS

Molecular dynamics simulations studies and free energy analysis on inhibitors of MDM2–p53 interaction

(2013) Rui-Juan Niu et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

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

(2013) Jinan Wang et al.   PLoS One

Misfolding of a polyalanine variant due to lack of electrostatic polarization effects

(2013) Tiedong Sun et al.   THEORETICAL CHEMISTRY ACCOUNTS

Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein

(2012) Zhili Zuo et al.   BIOPOLYMERS

Computational Studies of Difference in Binding Modes of Peptide and Non-Peptide Inhibitors to MDM2/MDMX Based on Molecular Dynamics Simulations

(2012) Jianzhong Chen et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Interaction of I50V Mutant and I50L/A71V Double Mutant HIV-Protease with Inhibitor TMC114 (Darunavir): Molecular Dynamics Simulation and Binding Free Energy Studies

(2012) Biswa Ranjan Meher et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

(2012) Tong Zhu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Simulating Molecular Mechanisms of the MDM2-Mediated Regulatory Interactions: A Conformational Selection Model of the MDM2 Lid Dynamics

(2012) Gennady M. Verkhivker   PLoS One

Activation of the p53 pathway by small-molecule-induced MDM2 and MDMX dimerization

(2012) B. Graves et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Elevated MDM2 boosts the apoptotic activity of p53-MDM2 binding inhibitors by facilitating MDMX degradation

(2011) Mingxuan Xia et al.   CELL CYCLE

Performance Assessment of Semiempirical Molecular Orbital Methods in Describing Halogen Bonding: Quantum Mechanical and Quantum Mechanical/Molecular Mechanical-Molecular Dynamics Study

(2011) Mahmoud A. A. Ibrahim   Journal of Chemical Information and Modeling

Fast and accurate computation schemes for evaluating vibrational entropy of proteins

(2011) Beisi Xu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular modeling and molecular dynamics simulation studies on pyrrolopyrimidine-based α-helix mimetic as dual inhibitors of MDM2 and MDMX

(2011) Shao-Yong Lu et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Insight into mechanism of small molecule inhibitors of the MDM2–p53 interaction: Molecular dynamics simulation and free energy analysis

(2011) Jianzhong Chen et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Polarization of Intraprotein Hydrogen Bond Is Critical to Thermal Stability of Short Helix

(2011) Ya Gao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Zinc Chelation with Hydroxamate in Histone Deacetylases Modulated by Water Access to the Linker Binding Channel

(2011) Ruibo Wu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

High affinity interaction of the p53 peptide-analogue with human Mdm2 and Mdmx

(2010) Anna Czarna et al.   CELL CYCLE

Differential binding of p53 and nutlin to MDM2 and MDMX: Computational studies

(2010) Thomas Leonard Joseph et al.   CELL CYCLE

Structures of low molecular weight inhibitors bound to MDMX and MDM2 reveal new approaches for p53-MDMX/MDM2 antagonist drug discovery

(2010) Grzegorz M. Popowicz et al.   CELL CYCLE

Calculations of the Free Energy of Interaction of the c-Fos−c-Jun Coiled Coil: Effects of the Solvation Model and the Inclusion of Polarization Effects

(2010) Zhili Zuo 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

A computational analysis of the binding model of MDM2 with inhibitors

(2010) Guodong Hu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular Dynamics Simulations on the Mechanism of Transporting Methylamine and Ammonia by Ammonium Transporter AmtB

(2010) Jinan Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Eu doping effects on structural and magnetic properties of (Sr2−xEux)FeMoO6 compounds

(2010) Q. Zhang et al.   JOURNAL OF SOLID STATE CHEMISTRY

Electrostatic Polarization Makes a Substantial Contribution to the Free Energy of Avidin−Biotin Binding

(2010) Yan Tong et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Folding of a Helix at Room Temperature Is Critically Aided by Electrostatic Polarization of Intraprotein Hydrogen Bonds

(2010) Li L. Duan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

D-peptide inhibitors of the p53-MDM2 interaction for targeted molecular therapy of malignant neoplasms

(2010) M. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The p53 orchestra: Mdm2 and Mdmx set the tone

(2010) Mark Wade et al.   TRENDS IN CELL BIOLOGY

Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations

(2009) Guo-Dong Hu et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Structure-based Design of High Affinity Peptides Inhibiting the Interaction of p53 with MDM2 and MDMX

(2009) Jason Phan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization

(2009) Li L. Duan et al.   JOURNAL OF CHEMICAL PHYSICS

Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential

(2009) Dian Jiao et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Theoretical Analysis of Kinetic Isotope Effects on Proton Transfer Reactions between Substituted α-Methoxystyrenes and Substituted Acetic Acids

(2009) Kin-Yiu Wong et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Simulation of NMR Data Reveals That Proteins’ Local Structures Are Stabilized by Electronic Polarization

(2009) Yan Tong et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX

(2009) M. Pazgier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Selectivity of Neutral/Weakly Basic P1 Group Inhibitors of Thrombin and Trypsin by a Molecular Dynamics Study

(2008) Emilia L. Wu et al.   CHEMISTRY-A EUROPEAN JOURNAL

Molecular Dynamics—Solvated Interaction Energy Studies of Protein–Protein Interactions: The MP1–p14 Scaffolding Complex

(2008) Qizhi Cui et al.   JOURNAL OF MOLECULAR BIOLOGY

Quantum Mechanical Studies of Residue-Specific Hydrophobic Interactions in p53−MDM2 Binding

(2008) Yun Ding et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein Polarization Is Critical to Stabilizing AF-2 and Helix-2′ Domains in Ligand Binding to PPAR-γ

(2008) C. G. Ji et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Temporal activation of p53 by a specific MDM2 inhibitor is selectively toxic to tumors and leads to complete tumor growth inhibition

(2008) S. Shangary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Very fast prediction and rationalization of pKa values for protein-ligand complexes

(2008) Delphine C. Bas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS