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

Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics

(2014) Yu-ming M. Huang et al.   JOURNAL OF MOLECULAR RECOGNITION

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

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

(2014) Mengyuan Liu et al.   Scientific Reports

Ligand selectivity of estrogen receptors by a molecular dynamics study

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

A Contribution to the Drug Resistance Mechanism of Darunavir, Amprenavir, Indinavir, and Saquinavir Complexes with HIV-1 Protease Due to Flap Mutation I50V: A Systematic MM–PBSA and Thermodynamic Integration Study

(2013) Georgios Leonis et al.   Journal of Chemical Information and Modeling

A Comparative Molecular Dynamics, MM–PBSA and Thermodynamic Integration Study of Saquinavir Complexes with Wild-Type HIV-1 PR and L10I, G48V, L63P, A71V, G73S, V82A and I84V Single Mutants

(2013) Haralambos Tzoupis et al.   Journal of Chemical Theory and Computation

Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model

(2013) Tong Zhu 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

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

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

Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir

(2012) Parimal Kar et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Origin of Decrease in Potency of Darunavir and Two Related Antiviral Inhibitors against HIV-2 Compared to HIV-1 Protease

(2012) Parimal Kar et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Critical differences in HIV-1 and HIV-2 protease specificity for clinical inhibitors

(2012) Yunfeng Tie et al.   PROTEIN SCIENCE

An overview of the Amber biomolecular simulation package

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

Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA

(2011) Samuel Genheden et al.   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

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

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

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

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

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

Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization

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

In Vitro Phenotypic Susceptibility of Human Immunodeficiency Virus Type 2 Clinical Isolates to Protease Inhibitors

(2008) D. Desbois et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Inhibition of HIV-2 Protease by HIV-1 Protease Inhibitors in Clinical Use

(2008) Evan T. Brower et al.   Chemical Biology & Drug Design

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

Structural Evidence for Effectiveness of Darunavir and Two Related Antiviral Inhibitors against HIV-2 Protease

(2008) Andrey Y. Kovalevsky 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

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

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

Design of HIV Protease Inhibitors Targeting Protein Backbone: An Effective Strategy for Combating Drug Resistance

(2007) Arun K. Ghosh et al.   ACCOUNTS OF CHEMICAL RESEARCH

Molecular Dynamics Simulations of Hemoglobin A in Different States and Bound to DPG: Effector-Linked Perturbation of Tertiary Conformations and HbA Concerted Dynamics

(2007) Monique Laberge et al.   BIOPHYSICAL JOURNAL

HIV-1 protease inhibitors: effects on HIV-2 replication and resistance

(2007) Luis Menéndez-Arias et al.   TRENDS IN PHARMACOLOGICAL SCIENCES