Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software

VirtualToxLab™ - In silico prediction of the toxic (endocrine-disrupting) potential of drugs, chemicals and natural products. Two years and 2,000 compounds of experience: a progress report

(2016) Angelo Vedani   ALTEX-Alternatives to Animal Experimentation

Reactions and enzymes in the metabolism of drugs and other xenobiotics

(2012) Bernard Testa et al.   DRUG DISCOVERY TODAY

Computational tools and resources for metabolism-related property predictions. 2. Application to prediction of half-life time in human liver microsomes

(2012) Alexey V Zakharov et al.   Future Medicinal Chemistry

2D SMARTCyp Reactivity-Based Site of Metabolism Prediction for Major Drug-Metabolizing Cytochrome P450 Enzymes

(2012) Ruifeng Liu et al.   Journal of Chemical Information and Modeling

RS-Predictor Models Augmented with SMARTCyp Reactivities: Robust Metabolic Regioselectivity Predictions for Nine CYP Isozymes

(2012) Jed Zaretzki 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

National prescription for drug development

(2012) Meredith Wadman   NATURE BIOTECHNOLOGY

In Silico Modeling of P450 Substrates, Inhibitors, Activators, and Inducers

(2011) Robert Kirk DeLisle et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Comparison of Metabolic Soft Spot Predictions of CYP3A4, CYP2C9 and CYP2D6 Substrates Using MetaSite and StarDrop

(2011) Young G. Shin et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Methodologies for Investigating Drug Metabolism at the Early Drug Discovery Stage: Prediction of Hepatic Drug Clearance and P450 Contribution

(2011) Chie Emoto et al.   CURRENT DRUG METABOLISM

In-Silico ADME Models: A General Assessment of their Utility in Drug Discovery Applications

(2011) M. Paul Gleeson et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Evaluation of Three State-of-the-Art Metabolite Prediction Software Packages (Meteor, MetaSite, and StarDrop) through Independent and Synergistic Use

(2011) H. T'jollyn et al.   DRUG METABOLISM AND DISPOSITION

In silicosite of metabolism prediction of cytochrome P450-mediated biotransformations

(2011) Ákos Tarcsay et al.   Expert Opinion on Drug Metabolism & Toxicology

Analysis of Commercial and Public Bioactivity Databases

(2011) Pekka Tiikkainen et al.   Journal of Chemical Information and Modeling

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

PubChem's BioAssay Database

(2011) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Patrik Rydberg et al.   ACS Medicinal Chemistry Letters

Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse

(2010) Lars Carlsson et al.   BMC BIOINFORMATICS

Probing Small-Molecule Binding to Cytochrome P450 2D6 and 2C9: An In Silico Protocol for Generating Toxicity Alerts

(2010) Gianluca Rossato et al.   ChemMedChem

Using Open Source Computational Tools for Predicting Human Metabolic Stability and Additional Absorption, Distribution, Metabolism, Excretion, and Toxicity Properties

(2010) R. R. Gupta et al.   DRUG METABOLISM AND DISPOSITION

Trainable structure–activity relationship model for virtual screening of CYP3A4 inhibition

(2010) Remigijus Didziapetris et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Probing Small-Molecule Binding to the Liver-X Receptor: A Mixed-Model QSAR Study

(2010) Morena Spreafico et al.   Molecular Informatics

The Comparative Toxicogenomics Database: update 2011

(2010) A. P. Davis et al.   NUCLEIC ACIDS RESEARCH

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

Estimation of reliability of predictions and model applicability domain evaluation in the analysis of acute toxicity (LD50)

(2010) A. Sazonovas et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

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

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

Probabilistic Prediction of the Human CYP3A4 and CYP2D6 Metabolism Sites

(2009) Justas Dapkunas et al.   CHEMISTRY & BIODIVERSITY

CypScore: Quantitative Prediction of Reactivity toward Cytochromes P450 Based on Semiempirical Molecular Orbital Theory

(2009) Matthias Hennemann et al.   ChemMedChem

Computational approaches to predict drug metabolism

(2009) Paul Czodrowski et al.   Expert Opinion on Drug Metabolism & Toxicology

Trend Analysis of a Database of Intravenous Pharmacokinetic Parameters in Humans for 670 Drug Compounds

(2008) R. S. Obach et al.   DRUG METABOLISM AND DISPOSITION

Cytochromes P450: A Structure-Based Summary of Biotransformations Using Representative Substrates

(2008) Caitlin M. Brown et al.   DRUG METABOLISM REVIEWS

Generation of a Set of Simple, Interpretable ADMET Rules of Thumb

(2008) M. Paul Gleeson   JOURNAL OF MEDICINAL CHEMISTRY

Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks

(2008) A. P. Davis et al.   NUCLEIC ACIDS RESEARCH

In Silico Tools for Sharing Data and Knowledge on Toxicity and Metabolism: Derek for Windows, Meteor, and Vitic

(2008) Carol A. Marchant et al.   TOXICOLOGY MECHANISMS AND METHODS