Databases, Datasets

 

  • HOBA - Collects human oral bioavailability for more than 1000 drugs (as reported by Wang & Hou in ADD-reviews, early 2015). Many other data on pKa, solubility, Caco-2, plasma binding, volume of distribution, toxicity, LD50, metabolism, urinary excretion... - database
  • openFDA - Open-source APIs and a developer community for FDA data - database
  • WITHDRAWN - A resource for withdrawn and discontinued drugs - database
  • MBROLE 2 - MBROLE - Metabolites Biological Role (pronounced as "embrole") performs overrepresentation (enrichment) analysis of categorical annotations for a set of compounds of interest.These categorical annotations correspond to biological and chemical information available in a number of public databases and software - database
  • LTKB - Liver Toxicity Knowledge Base. (see also via PubMed) DILIrank: the largest reference drug list ranked by the risk for developing drug-induced liver injury in humans - database
  • MutAIT - An online genetic toxicology data portal and analysis tools - database
  • hERGCentral - hERGCentral is a resource center for researchers who work on hERG potassium channels or develop therapeutic compounds without side cardiac effects (2015) - online
  • MetaboAnalyst - MetaboAnalyst 3.0: making metabolomics more meaningful - database
  • ADReCS - An ontology database for aiding standardization and hierarchical classification of adverse drug reaction terms - database
  • Metrabase - The Metabolism and Transport Database is a cheminformatics and bioinformatics resource that contains curated data related to human small molecule metabolism and transport - database
  • MRLs - Minimal risk levels Toxic Substances Portal - dataset
  • CCRIS - Chemical carcinogenesis research information system (mice, rats, ames salmonella typhimurium, human) for over 8000 compounds - dataset
  • ECOTOX - ECOTOXicology database provides single chemical toxicity information for aquatic and terrestrial life - dataset
  • EXTOXNET - The EXtension TOXicology NETwork (related to pesticide toxicology) - dataset
  • Poisonous - FDA Poisonous Plant Database - dataset
  • GeneTox - Genetic Toxicology Data Bank (GENE-TOX) - dataset
  • HERA - Human and Environmental Risk Assessment on Ingredients and Household Cleaning Products - dataset
  • IRIS - EPA's Integrated Risk Information System is a human health assessment program that evaluates information on health effects that may result from exposure to environmental contaminants - dataset
  • ITER - A database of human health risk values and cancer classifications for over 680 chemicals. (ITER can be search via TOXNET) - dataset
  • JECDB - Japan Existing Chemical Data Base (toxicity) - dataset
  • NPIC - National Pesticide Information Center - dataset
  • NTP - US NIH/NIEHS NationalToxicology Program testing - dataset
  • PAN Pesticide - Database - toxicity and regulatory information for pesticides - dataset
  • TEXTRATOX - The TETRATOX database is a collection of toxic potency data for more than 2400 industrial organic compounds (TEXTRATOX A collection of aquatic toxic potency data) - dataset
  • LINCS - LINCS canvas Browser: Interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures - Online
  • LINCS - LINCS aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents, and by using computational tools to integrate this diverse information into a comprehensive view of normal and disease states that can be applied for the development of new biomarkers and therapeutics. By generating and making public data that indicates how cells respond to various genetic and environmental stressors, the LINCS project will help gain a more detailed understanding of cell pathways and aid efforts to develop therapies that might restore perturbed pathways and networks to their normal states - online
  • EDCs DataBank - 3D-Structure database of endocrine disrupting chemicals - database
  • hERG - hERG related risk assessment of botanicals - database
  • ISSCAN - A curated database representative of “classical” carcinogens, largely consisting of industrial and laboratory chemicals, with a majority of genotoxic carcinogens. Check for new ones at OECD QSAR Toolbox - database
  • Open TG-GATEs - Open TG-GATEs is a public toxicogenomics database - database
  • NCTRlcdb - NCTR Liver Cancer Database (contains about 999 chemicals with liver carcinogenicity annotations) - database
  • Drug-drug - The DDI corpus: an annotated corpus with pharmacological substances and drug-drug interactions - database
  • hERGAPDbase - A database documenting hERG channel inhibitory potentials and APD-prolongation activities of chemical compounds - database
  • BioModels - Serves as a reliable repository of computational models of biological processes (for instance hERG mutations) - database of models
  • OCHEM - OCHEM contains for instance hERG datasets - dataset
  • QT drugs - QT drugs (involves hERG), information about drugs and some aspects of cardiotoxicity - dataset
  • SADS - Sudden arrhythmic death syndrome (e.g., herg). List of drugs to avoid - dataset
  • MACiE - Mechanism, Annotation and Classification in Enzymes (metalloproteins, Metal MACiE, a database of catalytic metal ions, with a view to understanding the functions of the roles and activity of catalytic metals in enzymes) - database
  • Selleckchem - Chemical compounds some with numerous annotations (including preclinical data), some dedicated to targets... - database
  • PharmaADME - According to PharmaADME database, ADME core genes are defined as the most important genes in drug metabolism, while ADME extended genes also play roles in drug metabolism but are relatively not essential as those core genes. About 32 core ADME genes and 250 extended ADME gene can be found (Jing Li et al, J Med Genetics 2014, PMID: 25074363) - database
  • hERG - hERG datasets (from Braga et al, Current Topics in Med Chem 2014) can be found at ChemBench - datasets
  • hERG - hERG datasets (from Braga et al, Current Topics in Med Chem 2014) can be found at LabMol. Unclear if the service is still running - datasets
  • FADB - Food Additive Molecular Database for in silico screening in food toxicology - contact the authors
  • Orange Book - Approved Drug Products with Therapeutic Equivalence Evaluations - database
  • Hepatotoxicity - Human Hepatotoxicity Database Suitable for QSAR Modeling Using Post-Market Safety Data - datasets available in the supplement of the article
  • tox-portal.net - Tox-Database.net: a curated resource for data describing chemical triggered in vitro cardiac ionchannels inhibition (hERG) - Database
  • PPD - Plasma Proteome Database. This database contains information on 10 546 proteins detected in serum/plasma of which 3784 have been reported in two or more studies - Database
  • CYP - P450 Drug Interaction Table - database
  • Transformer (biotransformation of xenobiotics) - The simultaneous administration of several drugs can cause severe adverse effects based on interactions with the same metabolizing enzyme(s). The Transformer database contains integrated information on the three phases of biotransformation (modification, conjugation and excretion) of 3000 drugs and >350 relevant food ingredients (e.g. grapefruit juice) and herbs, which are catalyzed by 400 proteins. A total of 100 000 interactions were found through text mining and manual validation. The 3D structures of 200 relevant proteins are included - Database
  • 3DMET - A database collecting three-dimensional structures of natural metabolites - database
  • Link - Trend analysis of a database of intravenous pharmacokinetic parameters in humans for 670 drug compounds by Obach RS, Franco Lombardo and Nigel J. Waters (Drug Metab Dispos. 2008 Jul;36(7):1385-405) - dataset (670 molecules)
  • Link - List of chemistry and tox databases - Database
  • Database - QSPR-THESAURUS Contains physico-chemical data and models for four classes of compounds (CADASTER) - database
  • hERG - hERG molecules inside the ChEMBL database - datasets
  • TOXBANK - Supporting integrated data analysis and servicing of alternative testing methods in toxicology, establishes a dedicated web-based warehouse for toxicity data management and modelling, a gold standards compound database and repository of selected test compounds, and a reference resource for cells, cell lines and tissues of relevance for in vitro systemic toxicity research carried out across the FP7 HEALTH.2010.4.2.9 Alternative Testing Strategies SEURAT program - Database
  • DrugMatrix -  The largest molecular toxicology reference database and informatics system - database
  • ToxRefDb - Toxicity Reference Database captures thousands of in vivo animal toxicity studies on hundreds of chemicals - database
  • HESS - Hazard Evaluation Support System Integrated Platform and the attached database (HESS DB), supports the evaluation of repeated dose toxicity by category approach - database
  • Cosmos - Integrated in silico models for the prediction of human repeated dose toxicity of Cosmetics to optimise safety - database
  • ChEMBLSpace -   Java application for the visual exploration and analysis of the chemogenomic space extracted from the ChEMBL database - standalone
  • Link - Ferenczy and Keseru, how fragments are optimized, 2013 - dataset of fragments and optimized compounds
  • Lead optimization - Emanuele Perola An Analysis of the Binding Efficiencies of Drugs and Their Leads in Successful Drug Discovery Programs J Med Chem 2010, Supporting Info, leads and corresponding drugs in SDF - dataset of lead and optimized leads
  • EBI - The EBI has a developed and maintained a number of protein structure related databases. The Protein Databank in Europe (PDBe) group, within the EBI, is responsible for the deposition and validation of new protein structures -  database
  • Brenda - The Comprehensive Enzyme Information System -  database
  • Enzyme - EnzymeDetector: Predict enzyme - online
  • Top 200 drugs - Top 200 prescriptions in 2002 (structure and name of the compounds). Prescription drug. Drug Index - Prescribed drugs, online
  • Link - Prescription drugs (structure and name of the compounds). Molecule of the month - Prescription drugs, online
  • FDA - FDA approved drugs - Database
  • Link - Chemical databases - Databases
  • SuperDrug - Contains 2.396 compounds. 3D-structures of active ingredients of essential marketed drugs. To account for structural flexibility they are represented by 10(5) structural conformers - Database
  • FDA - Drug@FDA - Database
  • SWEETLEAD - Database of Approved Drugs, Regulated Chemicals, and Herbal Isolates for Computer-Aided Drug Discovery - database to download
  • DrugBank - DrugBank, list of drugs, experimental structures...In 2014, many novel information about drug metabolism - database
  • CPI-Predictor -  Molecular polypharmacology, off-targets and drug repositioning focused on G protein-coupled receptors and kinome - online
  • Drug3k - Prescription drug information for consumers - online
  • Link - Compilation of web sites that offer chemistry databases/search services, data about toxic molecules, hazardous substances, database browser, Enhanced NCI Database Browser 2.1 - Databases
  • Link - A free database of commercially available solvents searchable by many properties - Database
  • Chembl - Database of bioactive molecules - Database
  • GOSTAR -  Online database product of GVK BIO. It is the largest manually curated SAR database that contains all the Published and Patented inhibitors against most biological targets and their associated SAR data. GOSTAR database contains compounds from both Discovery and Development along with associated SAR, ADME, Toxicity, and Pharmacokinetic Data. The database contains over 6 million inhibitors and over 14.9 million quantitative SAR points screened from around 2.1 million patents and 296,000 journals - commercial database
  • ChemID Plus - Chemical name, physical and toxicological properties - Database
  • 3DMET - Database of 3D structures of natural metabolites. The current version includes most of the natural products of the KEGG COMPOUND collection - Database
  • HIM-herbal ingredients - HIM-herbal ingredients in-vivo metabolism database. Various Links were made to PubChem, PubMed, TCM-ID (Traditional Chinese Medicine Information database) and HIT (Herbal ingredients' targets databases) - database
  • BiGG Database - A metabolic reconstruction of human metabolism designed for systems biology simulation and metabolic flux balance modeling - database
  • BioSM - A cheminformatics tool that uses known endogenous mammalian biochemical compounds (as scaffolds) and graph matching methods to identify endogenous mammalian biochemical structures in chemical structure space - online
  • MetaboLights -  An open access general purpose repository for metabolomics studies and associated meta-data - Database
  • Human Metabolome Database - Contains information about small molecule metabolites found in the human body, the database (version 3.0) contains 40278 metabolite entries - Database
  • HML - The Human Metabolome Library - Database
  • antiSMASH 2.0 - A versatile platform for genome mining of secondary metabolite producers (Microbial secondary metabolites are a potent source of antibiotics and other pharmaceuticals) - Database
  • T3DB - Toxin and Toxin Target Database is a unique bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. See also at this site: (see also at this site: Animal Toxin Database (ATDB), The Toxicology Data Network (TOXNET), The Comparative Toxicogenomics Database (CTD), The Aggregated Computation Toxicology Resource (ACToR), and SuperToxic - Database
  • e-Drug3D -  It offers a facility to explore FDA approved drugs - Database
  • MetaCyc -  A database of nonredundant, experimentally elucidated metabolic pathways - Database
  • BioMeta -  A database of metabolites and metabolic reactions. Its contents are largely based on the KEGG Ligand database. Compared to the KEGG database, a large number of chemical structures have been corrected with respect to constitution and stereochemistry - Database
  • KNApSAcK - A Comprehensive Species-Metabolite Relationship Database, compounds are in 3D with curated stereochemistry, natural products - Database
  • Link - Drug information portal - Prescribed drugs, drug information, online
  • Link - drugs.com - Prescribed drugs, drug information, online
  • DailyMed -  Provides high quality information about marketed drugs - Prescribed drugs, drug information, online
  • CYPED - The CYPED database integrates information on sequence and structure of cytochrome P450 monooxygenases to facilitate protein engineering - Database
  • ChEBI - Chemical Entities of Biological Interest is a freely available dictionary of molecular entities focused on small chemical compounds - Database
  • Link - The ADME databases - Database
  • FragmentStore -  A comprehensive database of fragments Linking metabolites, toxic molecules and drugs - database. Possible off-target interactions - Database
  • Link - A database for facilitating the search for drug Absorption, Distribution, Metabolism, Excretion associated proteins. It contains information about known drug ADME associated proteins, functions, similarities, substrates / ligands, tissue distributions, and other properties of the targets. Over 320 proteins - Database
  • ADME DB -  A database containing the latest and most comprehensive data on interactions of substances with Drug Metabolizing Enzymes and Drug Transporters - Databases
  • DSSTox - Distributed Structure-Searchable Toxicity Database Network (Richard and Williams 2002; Richard et al. 2002). Check also ACToR at www.epa.gov - Databases
  • Toxnet - Databases on toxicology, hazardous chemicals, environmental health, and toxic releases, find information about molecules - Databases
  • Link - Toxnet, HSDB, Hazardous substances data bank - Databases
  • DITOP - Drug-Induced Toxicity Related Proteins - Databases
  • INCHEM - Chemical Safety Information from Intergovernmental Organizations - Databases
  • SuperToxic - In order to facilitate drug design, toxic compounds were collected from literature and web sources in this database - Database
  • SuperCyp - This database contains about 1,170 drugs, 2,785 Cytochrome-Drug interactions and about 1,200 alleles, check also other Links there, prodrugs, Phase 2 enzymes, drugs... - database
  • SuperHapten - An Immunogenic Compound Database This database contains currently 7257 haptens, 453 commercially available related antibodies and 24 carriers - database
  • Toxicoinformatics - Toxicoinformatics database at the FDA (application of systems biology to ADME/Tox). See also Leadscope (commercial) -  database
  • Link - DART (Ji et al. 2003), ADME-AP (Sun et al. 2002), TRMP (Zheng et al. 2004), TTD (Chen et al. 2002a): databases for facilitating the search for drug Absorption, Distribution, Metabolism, Excretion associated proteins. Therapeutic Target Database (268 successful targets in TTD in May 2007) - Databases
  • Link - Metabolomics database - online
  • PHYSPROP -  Contains chemical structures, names and physical properties for over 25,000 compounds - Chemistry database
  • Link - Cancer expert system, carcinogenicity..., EPA, datasets, online tools... - datasets
  • CPDB - The Carcinogenic Potency Database. The Database is a unique and widely used international resource of the results of 6540 chronic, long-term animal cancer tests on 1547 chemicals. - datasets
  • OpenTox -  Community site - ADME/tox ...
  • eChemPortal -  Provides free public access to information on properties of chemicals: Physical Chemical Properties Ecotoxicity Environmental Fate and Behaviour Toxicity - datasets
  • Link - PK/DB is a free database and predictive service for researches - database
  • Link - This database is an attempt to catalog in a convenient, searchable fashion all publicly available information about the identities of mammalian proteins that become covalently adducted by chemically-reactive metabolites of xenobiotic agents including drugs - database
  • TETRATOX - The database is a collection of toxic potency data for more than 2,400 industrial organic compounds of which more than 1,600 have been published - database
  • admetSAR -  Models and databases: provides the manually curated data for diverse chemicals associated with known Absorption, Distribution, Metabolism, Excretion and Toxicity profiles - datasets
  • MetaADEDB - MetaADEDB databases - databases
  • MetaADEDB - MetaADEDB databases - databases
  • Link - Chemistry blog - melting point... - Chemistry blog
  • C-ChemBench - The Carolina Cheminformatics Workbench is an integrated toolkit developed by the Carolina Exploratory Center for Cheminformatics Research (CECCR) with the support of the National Institutes of Health. Chembench is a free portal that enables researchers to mine available chemical and biological data - Chemistry tools, online
  • Link - Oral administered drugs are mainly absorbed in the small intestine. Here, depending on drug composition and size, absorption can happen through a variety of processes...Drug Discovery with Quantum Pharmaceuticals - Blog ADME and drug design
  • PKKB - PharmacoKinetics Knowledge Base is the most extensive freely available database for collecting ADME (Absorption, Distribution, Metabolism, and Excretion) and Toxic properties - datasets
  • Phospholipidosis - The phospholipidosis dataset of 182 compounds, Lowe et al. Journal of Cheminformatics 2012 4:2 - dataset
  • Phospholipidosis - Phospholipidosis dataset, Mol. Pharmaceutics, 2010, 7 (5), pp 1708-1714 - dataset
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