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Databases, Datasets, ADMET related

 

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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WITHDRAWN A resource for withdrawn and discontinued drugs database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