Effects of protein flexibility and active site water molecules on the prediction of sites of metabolism for cytochrome P450 2C19 substrates

Prediction of cytochrome P450 mediated metabolism

(2015) Lars Olsen et al.   ADVANCED DRUG DELIVERY REVIEWS

The impact of molecular dynamics on drug design: applications for the characterization of ligand–macromolecule complexes

(2015) Jérémie Mortier et al.   DRUG DISCOVERY TODAY

Evidence of Water Molecules—A Statistical Evaluation of Water Molecules Based on Electron Density

(2015) Eva Nittinger et al.   Journal of Chemical Information and Modeling

Predicting the binding modes and sites of metabolism of xenobiotics

(2015) Goutam Mukherjee et al.   Molecular BioSystems

Predicting drug metabolism: experiment and/or computation?

(2015) Johannes Kirchmair et al.   NATURE REVIEWS DRUG DISCOVERY

Beware of docking!

(2015) Yu-Chian Chen   TRENDS IN PHARMACOLOGICAL SCIENCES

Survey of Human Oxidoreductases and Cytochrome P450 Enzymes Involved in the Metabolism of Xenobiotic and Natural Chemicals

(2014) Slobodan Rendic et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Elucidating Substrate Promiscuity in the Human Cytochrome 3A4

(2014) Christina Hayes et al.   Journal of Chemical Information and Modeling

POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics

(2014) Jacob D. Durrant et al.   Journal of Chemical Theory and Computation

Effects of protein flexibility on the site of metabolism prediction for CYP2A6 substrates

(2014) Yayun Sheng et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Combining Structure- and Ligand-Based Approaches to Improve Site of Metabolism Prediction in CYP2C9 Substrates

(2014) Laura J. Kingsley et al.   PHARMACEUTICAL RESEARCH

Prediction of Cytochrome P450 Xenobiotic Metabolism: Tethered Docking and Reactivity Derived from Ligand Molecular Orbital Analysis

(2013) Jonathan D. Tyzack et al.   Journal of Chemical Information and Modeling

DR-Predictor: Incorporating Flexible Docking with Specialized Electronic Reactivity and Machine Learning Techniques to Predict CYP-Mediated Sites of Metabolism

(2013) Tao-wei Huang et al.   Journal of Chemical Information and Modeling

XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with Neural Networks

(2013) Jed Zaretzki et al.   Journal of Chemical Information and Modeling

The Contribution of Atom Accessibility to Site of Metabolism Models for Cytochromes P450

(2013) Patrik Rydberg et al.   MOLECULAR PHARMACEUTICS

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

Comparison of Cytochrome P450 2C Subfamily Members in Terms of Drug Oxidation Rates and Substrate Inhibition

(2012) Toshiro Niwa et al.   CURRENT DRUG METABOLISM

Structural Characterization of Human Cytochrome P450 2C19

(2012) R. Leila Reynald et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Development of a Computational Tool to Rival Experts in the Prediction of Sites of Metabolism of Xenobiotics by P450s

(2012) Valérie Campagna-Slater et al.   Journal of Chemical Information and Modeling

Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms

(2012) Johannes Kirchmair et al.   Journal of Chemical Information and Modeling

Potentially increasing the metabolic stability of drug candidates via computational site of metabolism prediction by CYP2C9: The utility of incorporating protein flexibility via an ensemble of structures

(2011) Matthew L. Danielson et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

RS-Predictor: A New Tool for Predicting Sites of Cytochrome P450-Mediated Metabolism Applied to CYP 3A4

(2011) Jed Zaretzki et al.   Journal of Chemical Information and Modeling

IDSite: An Accurate Approach to Predict P450-Mediated Drug Metabolism

(2011) Jianing Li et al.   Journal of Chemical Theory and Computation

Structure-Based Site of Metabolism Prediction for Cytochrome P450 2D6

(2011) Samuel L. C. Moors et al.   JOURNAL OF MEDICINAL CHEMISTRY

The SMARTCyp cytochrome P450 metabolism prediction server

(2010) Patrik Rydberg et al.   BIOINFORMATICS

Structural diversity of cytochrome P450 enzyme system

(2010) Tsuneo Omura   JOURNAL OF BIOCHEMISTRY

ChemSpider: An Online Chemical Information Resource

(2010) Harry E. Pence et al.   JOURNAL OF CHEMICAL EDUCATION

ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers

(2010) K. Shawn Watts et al.   Journal of Chemical Information and Modeling

SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism

(2010) Patrik Rydberg et al.   ACS Medicinal Chemistry Letters

Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6

(2009) Rita Santos et al.   Journal of Chemical Information and Modeling

Reduced Catalytic Activity of P450 2A6 Mutants with Coumarin: A Computational Investigation

(2009) Weihua Li et al.   Journal of Chemical Theory and Computation

SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions

(2009) Saskia Preissner et al.   NUCLEIC ACIDS RESEARCH

PubChem: a public information system for analyzing bioactivities of small molecules

(2009) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

The Effect of CYP2C19 Polymorphism on the Pharmacokinetics and Pharmacodynamics of Clopidogrel: A Possible Mechanism for Clopidogrel Resistance

(2008) KA Kim et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450

(2008) Eva Stjernschantz et al.   Expert Opinion on Drug Metabolism & Toxicology

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

Cytochrome P450 and Chemical Toxicology

(2007) F. Peter Guengerich   CHEMICAL RESEARCH IN TOXICOLOGY