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

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

Predicting Drug Metabolism by Cytochrome P450 2C9: Comparison with the 2D6 and 3A4 Isoforms

(2012) Patrik Rydberg et al.   ChemMedChem

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

Risk assessment and mitigation strategies for reactive metabolites in drug discovery and development

(2010) Richard A. Thompson et al.   CHEMICO-BIOLOGICAL INTERACTIONS

Computer-aided drug design platform using PyMOL

(2010) Markus A. Lill et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

POVME: An algorithm for measuring binding-pocket volumes

(2010) Jacob D. Durrant et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

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

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

Fast Prediction of Cytochrome P450 Mediated Drug Metabolism

(2009) Patrik Rydberg et al.   ChemMedChem

Seeking the soft spots

(2009) Peter Kirkpatrick   NATURE REVIEWS DRUG DISCOVERY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Prediction of Metabolism by Cytochrome P450 2C9: Alignment and Docking Studies of a Validated Database of Substrates

(2008) Matthew J. Sykes et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

Metabolic Soft Spot Identification and Compound Optimization in Early Discovery Phases Using MetaSite and LC-MS/MS Validation

(2008) Markus Trunzer et al.   JOURNAL OF MEDICINAL CHEMISTRY