Molecular Dynamics of CYP2D6 Polymorphisms in the Absence and Presence of a Mechanism-Based Inactivator Reveals Changes in Local Flexibility and Dominant Substrate Access Channels

The role of cytochrome P450 2B6 and 2B4 substrate access channel residues predicted based on crystal structures of the amlodipine complexes

(2014) Hyun-Hee Jang et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Potent Mechanism-Based Inactivation of Cytochrome P450 2B4 by 9-Ethynylphenanthrene: Implications for Allosteric Modulation of Cytochrome P450 Catalysis

(2013) Haoming Zhang et al.   BIOCHEMISTRY

Conformational diversity and ligand tunnels of mammalian cytochrome P450s

(2013) Xiaofeng Yu et al.   BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY

In Silieo Study on the Inhibitory Interaction of Drugs with Wild-type CYP2D6.1 and the Natural Variant CYP2D6.17

(2013) Koichi Handa et al.   Drug Metabolism and Pharmacokinetics

CYP 2D6 Binding Affinity Predictions Using Multiple Ligand and Protein Conformations

(2013) Lovorka Perić-Hassler et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Structural Diversity of Eukaryotic Membrane Cytochrome P450s

(2013) Eric F. Johnson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular Dynamic Investigations of the Mutational Effects on Structural Characteristics and Tunnel Geometry in CYP17A1

(2013) Ying-Lu Cui et al.   Journal of Chemical Information and Modeling

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Distal Effect of Amino Acid Substitutions in CYP2C9 Polymorphic Variants Causes Differences in Interatomic Interactions against (S)-Warfarin

(2013) Panida Lertkiatmongkol et al.   PLoS One

Is There a Relationship Between the Substrate Preferences and Structural Flexibility of Cytochromes P450?

(2012) Michal Otyepka et al.   CURRENT DRUG METABOLISM

Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P450 Probed by Molecular Dynamics Simulations

(2012) Tereza Hendrychova et al.   CURRENT DRUG METABOLISM

Crystal Structure of Human Cytochrome P450 2D6 with Prinomastat Bound

(2012) An Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Binding of quinidine radically increases the stability and decreases the flexibility of the cytochrome P450 2D6 active site

(2012) Karel Berka et al.   JOURNAL OF INORGANIC BIOCHEMISTRY

Mutation-Induced Loop Opening and Energetics for Binding of Tamiflu to Influenza N8 Neuraminidase

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

Molecular Modeling to Provide Insight into the Substrate Binding and Catalytic Mechanism of Human Biliverdin-IXα Reductase

(2012) Gang Fu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

(2012) Eva Chovancova et al.   PLoS Computational Biology

Comparison of Cytochrome P450 2D6 and Variants in Terms of Drug Oxidation Rates and Substrate Inhibition

(2011) Toshiro Niwa et al.   CURRENT DRUG METABOLISM

Substituted Imidazole of 5-Fluoro-2-[4-[(2-phenyl-1H-imidazol-5-yl)methyl]-1-piperazinyl]pyrimidine Inactivates Cytochrome P450 2D6 by Protein Adduction

(2011) L. D. Nagy et al.   DRUG METABOLISM AND DISPOSITION

Anandamide Oxidation by Wild-Type and Polymorphically Expressed CYP2B6 and CYP2D6

(2011) C. Sridar et al.   DRUG METABOLISM AND DISPOSITION

Long-Range Effects of a Peripheral Mutation on the Enzymatic Activity of Cytochrome P450 1A2

(2011) Tao Zhang et al.   Journal of Chemical Information and Modeling

Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle

(2011) Kiumars Shahrokh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

(2011) Enguerran Vanquelef et al.   NUCLEIC ACIDS RESEARCH

Two-dimensional NMR and All-atom Molecular Dynamics of Cytochrome P450 CYP119 Reveal Hidden Conformational Substates

(2010) Jed N. Lampe et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Mechanism of the decrease in catalytic activity of human cytochrome P450 2C9 polymorphic variants investigated by computational analysis

(2010) Eri Sano et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Prediction and analysis of the modular structure of cytochrome P450 monooxygenases

(2010) Demet Sirim et al.   BMC STRUCTURAL BIOLOGY

Polymorphism of Human Cytochrome P450 2D6 and Its Clinical Significance

(2009) Shu-Feng Zhou   CLINICAL PHARMACOKINETICS

New insights into the structural characteristics and functional relevance of the human cytochrome P450 2D6 enzyme

(2009) Bo Wang et al.   DRUG METABOLISM REVIEWS

Functional Characterization of 17 CYP2D6 Allelic Variants (CYP2D6.2, 10, 14A-B, 18, 27, 36, 39, 47-51, 53-55, and 57)

(2008) K. Sakuyama et al.   DRUG METABOLISM AND DISPOSITION

Impact of Plasticity and Flexibility on Docking Results for Cytochrome P450 2D6: A Combined Approach of Molecular Dynamics and Ligand Docking

(2008) Jozef Hritz et al.   JOURNAL OF MEDICINAL CHEMISTRY

Flexibility of Human Cytochromes P450: Molecular Dynamics Reveals Differences between CYPs 3A4, 2C9, and 2A6, which Correlate with Their Substrate Preferences

(2008) Josef Skopalík et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Insights into drug metabolism by cytochromes P450 from modelling studies of CYP2D6-drug interactions

(2007) J-D Maréchal et al.   BRITISH JOURNAL OF PHARMACOLOGY

Mechanism-Based Inactivation of Human Cytochromes P450s: Experimental Characterization, Reactive Intermediates, and Clinical Implications

(2007) Paul F. Hollenberg et al.   CHEMICAL RESEARCH IN TOXICOLOGY