ADMET and physchem predictions and related tools

  • AERS spider - An online interactive tool to mine statistical associations in Adverse Event Reporting System Pharmacoepidemiology and Drug Safety (2014) - online
  • CarcinoPred-EL - carcinogenicity of chemicals (2017) - online
  • Pred-hERG - Predict hERG - cardiotoxicity - online
  • Pred-Skin - Chemically-induced skin sensitization - online
  • SwissADME - Compute physicochemical descriptors as well as predict pharmacokinetics properties and druglike nature of one or multiple small molecules (BBB, Cyp, Pgp...) - online
  • Endocrine - Endocrine Disruptome (predicted by docking) - online
  • LIVERTOX - Search for hepatoxicity of drugs and herbs - database
  • QsarDB - QsarDB is a smart repository for (Q)SAR/QSPR models and datasets, ready for discovery, exploring, and citing - database
  • IDAAPM - Integrated database of ADMET and adverse effects of predictive modeling based on FDA approved drug data - database
  • DILI - DILIserver: Deep Learning for Drug-Induced Liver Injury, this has been the single most frequent cause of safety-related drug marketing withdrawals for the past 50 years (2015) - online
  • DILI - Pains and aggretators via Zinc (2016) - online
  • cactus - Metabolic stability, Half-life... - online
  • Pharmacist - Virtual Pharmacist: A Platform for Pharmacogenomics. A web-based platform that takes common types of high-throughput data, namely microarray SNP genotyping data, FASTQ and Variant Call Format (VCF) files as inputs, and reports potential drug responses in terms of efficacy, dosage and toxicity - online
  • Open - OpenVirtualToxLab: ADMET prediction, 16 proteins, known or suspected to trigger adverse effects are implemented at present: 10 nuclear receptors (androgen, estrogen a, estrogen b, glucocorticoid, liver X, mineralocorticoid, peroxisome proliferator-activated receptor g, progesterone, thyroid a, thyroid b), four members of the cytochrome P450 enzyme family (1A2, 2C9, 2D6, 3A4), a cytosolic transcription factor (aryl hydrocarbon receptor) and a potassium ion channel (hERG). (requires license, for non-profit organizations) (2015) - online
  • hERGCentral - hERGCentral is a resource center for researchers who work on hERG potassium channels or develop therapeutic compounds without side cardiac effects (2015) - online
  • SOMP - Site Of Metabolism Prediction (online). Prediction is based on PASS. For 1A2, 2C9, 2C19, 2D6 and 3A4 isoforms of cytochrome P450 and the SOMs of the all isoforms of UGT - online
  • SOM prediction - The present methodology is based on a combination of docking followed by molecular orbital (MO) calculations and knowledge based methods to predict the potential metabolic sites of a molecule and its metabolic products (Cytochrome P450s (CYPs)) (2015) - online
  • iPrior - Using Online Tool for Modeling ToxCast-TM Assays Towards Prioritization of Animal Toxicity Testing - online
  • PAINS-Remover - PAINS (pan assay interference compounds) is likely to interfere in screening technologies via a number of means but particularly through protein reactivity - online
  • MLViS - A Web Tool for Machine Learning-Based Virtual Screening in Early-Phase of Drug Discovery and Development. The tool can classify molecules as drug-like and nondrug-like based on various machine learning methods, including discriminant, tree-based, kernel-based, ensemble and other algorithms - online
  • XenoSite - Extending P450 site-of-metabolism models with region-resolution data - online
  • Chemo tools - Fraggle, the fragment store (search for fragments by drug names or PDB header). It provides property information (charge, hydrophobicity, and binding site preferences) and performs statistical analysis and can view the IDS of drugs and toxic compounds, which contain the fragments - online
  • CypRules - A rule-based P450 inhibition prediction server (2015) - online
  • Biozyne P-gp Predictor - Accurate models for P-gp drug recognition induced from a cancer cell line cytotoxicity screen - online, 1 cmpd at a time
  • Danish - Danish (Q)SAR Database. A repository of estimates from over 70 (Q)SAR models for 166,072 chemicals - database
  • CypRules - Descriptor and program files for all compounds are also publically available - standalone
  • SCYPPred - A web-based predictor of SNPs for human cytochrome P450 (2012) - online
  • AOP - Define adverse outcome pathways (AOPs) - online
  • AOP-XPlorer - Explore adverse outcome pathways (AOPs) - online
  • Effectopedia - It is an open-knowledge aggregation and collaboration tool designed to facilitate the interdisciplinary efforts for delineating adverse outcome pathways (AOPs) - online
  • IntSide - A web server for the chemical and biological examination of drug side effects - online
  • ToxPredict - ToxPredict (associated to OpenTox) - online
  • admetSAR - Models and databases: provides the manually curated data for diverse chemicals associated with known Absorption, Distribution, Metabolism, Excretion and Toxicity profiles. Many endpoints, hERG, CYP, PgP, oral, toxicity, AMES... - online
  • BADAPPLE - BioActivity Data Associative Promiscuity Pattern Learning Engine learns from “frequent hitters” found in the Molecular Libraries Screening program, and flags promiscuous compounds. New Promiscuity Engine Released (MLS) - online, may not work at present
  • pkcsm - Small-molecule pharmacokinetic and toxicity properties using graph-based signatures - online
  • HTS PAINS - Blog about promiscuous compounds. Warning, need to be read with caution because at present, we do not have a clear understanding about PAINS - online
  • HLP - The web server HLP has been developed for assisting the scientific community for predicting intestinal half-life of peptides and to design mutant peptides with better half-life and physicochemical properties. HLP models were trained using a dataset of peptides whose half-lives have been determined experimentally in crude intestinal proteases preparation. Thus, HLP server will help in designing peptides possessing the potential to be administered via oral route - online
  • eTOX - The eTOX Library of Public Resources for in Silico Toxicity Prediction - database
  • hERG - The hERG 1.0 server predicts cardiotoxicity of drug molecules - online
  • FAME - FAst MEtabolizer: A rapid and accurate predictor of sites of metabolism in multiple species by endogenous enzymes. FAME is freely available from the authors to academia and nonprofit organizations - standalone
  • EPA USA - T.E.S.T. estimates the toxicity values and physical properties of organic chemicals based on the molecular structure of the organic chemical entered by the user - standalone
  • 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) - online
  • ADME SARfari - Predict likely ADME targets for an input molecule, Find ADME targets similar to an input FASTA sequence, Find ADME targets related to text terms, Find pharmacokinetic data relating to an input target, sequence or text term, Find activity pharmacokinetic data for an input molecule or related compounds (via a similarity substructure search), Match expression levels in human tissues for found targets - online
  • DataWarrior - A nice free tool for Chemistry Aware Data Visualization and Analysis (openmolecules.org). From filtering compounds, to data analysis and computation of descriptors (eg, binned log P, log S, druglikeness score, rotatable bonds...automatic SAR, activity cliff, cluster compounds, find similar compounds...search fragments..look all your compounds, 2D, 3D, see physchem parameters...) (for Mac, Windows and Linux) - standalone
  • MCSS - A multi-fingerprint browser for the ZINC database. To confirm the activity of an initial small molecule hit compound from an activity screening, one needs to probe the structure–activity relationships by testing close analogs. The multi-fingerprint browser assists this process - online
  • DruLiTo - Predict drug-likeness of a compound - online
  • Tox-Comp.net - Prediction for hERG - standalone
  • ProTox - A web server for the in silico prediction of rodent oral toxicity - online
  • Alkemio - Association of chemicals with biomedical topics by text and data mining - online
  • METIS - The METIS (Metabolic Information Input System) Editor is a user-friendly open-source application designed for the storage and input of information on metabolism and degradation reactions in the database employed by the Chemical Reactivity and Fate Tool (CRAFT) software - standalone
  • CYPSI - A structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana - database
  • ACD/I-Lab - ADME-Tox prediction - online
  • SOMUGT - In silico site of metabolism prediction for human UGT-catalyzed reactions (2014) - standalone
  • Solubility - Development of Dimethyl Sulfoxide Solubility Models. The best models developed with the publicly available Enamine data set are freely available online - online
  • WhichCyp - Prediction of cytochromes P450 inhibition, a tool for prediction of which cytochromes P450 isoforms (among 1A2, 2C9, 2C19, 2D6 and 3A4) a given molecule is likely to inhibit. The models are built from experimental high-throughput data using support vector machines and molecular signatures - online and standalone
  • PPS - UM-BBD Pathway Prediction System. Webservice to predict plausible pathways for microbial degradation of chemical compounds. Predictions use biotransformation rules, based on reactions found in the UM-BBD database or in the scientific literature. A list of rules is available - online and standalone
  • MetaPrint2D - Metabolic site predictor. MetaPrint2D-React is a tool that predicts xenobiotic metabolism through data-mining and statistical analysis of known metabolic transformations reported in scientific literature - online
  • Aggregator Advisor - This is a free service to suggest molecules that aggregate or may aggregate under biochemical assay conditions - online
  • ToxCreate - Creates computational models to predict toxicity - online
  • Link - E. coli toxicity prediction web server based on QSAR models (Faulon's lab) - online, need to register
  • MedChem Designer - MedChem Designer 2.0, chemical drawing and ADMET prediction - standalone, need to register
  • AquaSol - Predict aqueous solubility of small molecules using UG-RNN ensembles - standalone
  • Vega-QSAR - Vega-QSAR.eu: Tools for qsar prediction of ADMET (ORCHESTRA is an EU project, funded to disseminate recent research on in silico (computer-based) methods for evaluating the toxicity of chemicals, REACH, courses); ANTARES, alternative to animal testing, CAESAR, EC funded project which was specifically dedicated to develop QSAR models for the REACH legislation - standalone
  • Natural Product Likeness - The Natural-Product-Likeness scoring system is also implemented as Taverna 2.2 workflows, and is available under Creative Commons Attribution-Share Alike 3.0 Unported License The present Link goes to the executable standalone java package (under Academic Free License) - standalone
  • HExpoChem - The server contains information on diverse sources of chemicals with the aim to explore human health risk from diverse chemicals exposure. Five sources of information are considered i.e. drugs, foods, cosmetics, industrial chemicals and human metabolites corresponding of 10183 unique chemicals with bioactivities for 19 483 human proteins. HExpoChem can help in the decision of potential proteins and proteins complexes associated to life-style diseases. It can assist also to the possible cumulative risk of chemicals that interact to a same set of proteins - online
  • QED - A webserver for quantitative estimating the drug-likeness of a molecule - online
  • DrugMint - Predict the druggabilty of a compound. This server has been developed on the basis of difference in descriptors of approved and experimental small molecules. This server will help in knowing the druggable properties of a chemical structure - online
  • SOMEViz - A web service for site of metabolism estimating and visualizing - online
  • Link - Elucidation of chemical-protein interactions (CPI) spectrum - online
  • Link - Computational resources for drug discovery: many tools for ADMET and also QSAR, virtual screening... - Links, online
  • PaDEL - PaDEL-DDPredictor: Calculate pharmacodynamics, pharmacokinetics and toxicological properties of compounds - standalone
  • Link - PreADME, drug-likeness, ADMET - standalone
  • Lilly Open Innovation ADMET - Rejection rules from Lilly Open Innovation Drug Discovery initiative (reactivity and promiscuity filters, drug similarity). Over 275 rules addressing a variety of possible reasons to reject a molecules and the BMS rules. Lilly-MedChem-Rules stand-alone distribution. Thanks to Greg Durst for pointing to the Lilly-MedChem-Rules stand-alone command line utility titled 'tsubstructure' which lets you search very large SMILES files for specific SMARTS queries - standalone in C
  • Eli Lilly Open Innovation - Rejection rules from Eli Lilly Open Innovation Drug Discovery initiative online (via Tripod project, a series of user-friendly chemical genomics browser developed by the informatics group at the NIH Chemical Genomics Center) (reactivity and promiscuity filters, drug similarity) - online
  • Mcule.com - Toxicity checker, Searching for substructures commonly found in toxic and promiscuous ligands, Based on more than 100 SMARTS toxic matching rules - Online
  • Mcule.com - Property calculator for one molecule (Create a physicochemical property profile) - Online
  • QSAR TOOLBOX - Software for grouping chemicals into categories and filling gaps in (eco)toxicity data needed for assessing the hazard of chemicals - standalone
  • ECOSAR - Ecological Structure Activity Relationships (windows) - standalone
  • Open PHACTS - The Open PHACTS Explorer allows multiple sources of publicly-available pharmacological and physicochemical data to be intuitively queried, and makes data provenance accessible at every step - database
  • RS-Web - RS-WebPredictor: Predict cytochrome P450 mediated sites of metabolism on drug-like molecules - online
  • ToxCast - Screening Chemicals to Predict Toxicity Faster and Better - database
  • DemQSAR - predicting human volume of distribution and clearance of drugs - online
  • Insilicofirst - Try Entering a Chemical into our Toxicity Prediction Software - .
  • FAF-Drugs2 and now FAF-drugs3 - Online ADMET filtering server, compound collection preparation, see the Link to the user guide just below. At present uses SDF as input, but can take SMILES for instance via the bank-formatter utility. The outputs can be directly piped into other services. New version FAF-Drugs3 2015 - Online
  • Link - FAF-Drugs2 (and now version 3) online ADMET filtering server, PAINS (molecules that can interfere with assays...see J Baell in J Med Chem)....Lagorce, Villoutreix et al, Bioinformatics 2011 - Chemistry tools, this is the user guide
  • ToxAlerts - Web server of structural alerts for toxic chemicals and compounds with potential adverse reactions. The database already contains almost 600 structural alerts for such endpoints as mutagenicity, carcinogenicity, skin sensitization, compounds that undergo metabolic activation, and compounds that form reactive metabolites and, thus, can cause adverse reactions, QSAR models can be built - online (OCHEM)
  • DDI-CPI - A server Predicting Drug-Drug Interaction via Chemical-Protein Interactome - online, you need registration
  • Myc - MycPermCheck: Online tool for permeability prediction of small molecules against Mycobacterium tuberculosis. Basis of the prediction program is a logistic regression model of the physico-chemical properties of permeable substances - Chemistry tools, online
  • Gusar - Gusar ecotoxicity - online
  • Gusar - Gusar antitargets, rat toxicity... - online
  • CoFFer - A QSAR web service that predicts chemical compounds and provides fragments to aid interpreting predictions. 76 (Q)SAR models (ADMET, off targets, repositioning..) - online
  • Gusar - Gusar acute rat toxicity prediction - online
  • ToxiPred - Prediction of aqueous toxicity of small chemical molecules in T. pyriformis - online
  • MDRIpred - Prediction of Inhibitor against Drug Resistant M.Tuberculosis - online
  • ChemBioServer - ChemBioServer compound filtering (Rule of 5...) - online
  • PharmBench - The aim of PharmBench is to provide a community benchmark dataset for the evaluation of molecular alignment and pharmacophore elucidation approaches, and also a webservice to help users evaluate their own methods.
    The dataset consists of 81 targets, containing 960 ligands in total - dataset
  • Filter-it - Filter-it and related, software packages to filter collections and many others, pharmacophore, extract molecular scaffolds, align shape... - standalone
  • BBB predictor - Online BBB predictor (Prof Xiang-Qun (Sean) Xie, Pitt.edu) - ADMET CNS BBB, online
  • MetaPred - Server predict metabolizing CYP isoform of a drug molecule/substrate, based on SVM models developed using CDK descriptors - online
  • MetaPrint2D - MetaPrint2D metabolic site predictor - online
  • PPS - Predicts plausible pathways for microbial degradation of chemical compounds - online
  • Link - ADME Calculator (metabolism) - online
  • OncoLogic - OncoLogic TM is a personal computer software Predicting cancer causing potential of a chemical - standalone
  • OSIRIS - OSIRIS Property Explorer - online
  • Link - Physical Property Estimation - online
  • Toxtree - Toxtree, ADMET, has also Cyp prediction via SMARTCyp (Cytochrome P450-Mediated Drug Metabolism) and prediction of compounds that might bind covalently to proteins - standalone
  • Toxtree - Toxtree, the online version - online
  • Toxtree - Application for grouping chemicals and for predicting various types of toxicity based on decision tree approaches. - standalone
  • Lazar - Lazy Structure-Activity Relationships is a tool for the prediction of toxic activities - online
  • VirtualToxLab - The VirtualToxLab, 3D ADME/tox - online
  • Link - Web service to estimate toxicological hazard of a chemical structure. Molecules can be drawn, or input by any identifier (CAS, Name, EINECS) or SMILES or InChI or URL of OpenTox compound or dataset - online
  • ACuteTox - ACuteTox (the project is done but some information ?) - online
  • DrugLogit - Predicting the probability of a compound being classified as a drug or non-drug, as well as disease category (or organ) classification - online
  • AlogP - Tools to predict logP (with several methods) - online
  • ZINC - Some ADME/tox filtering - online
  • Edetox - Find compound properties - Chemistry, online
  • Link - ADME/tox eyesopen, commercial and demo - ADME/tox, online
  • Molinspiration - ADME/tox Molinspiration, commercial and demo - online
  • ICM - ADME/tox molsoft, commercial and demo - online
  • Chemaxon - ADME/tox chemicalize - online
  • Link - ADME/tox online molecular-networks - online
  • Checkmol - Checkmol is a command-line utility program which reads molecular structure files in different formats - standalone
  • Smartsfilter - ADMET filtering (Glaxo, Oprea, Blake, Pains, NMR alert...) - Online
  • Link - FAF-Drugs: ADME/tox online, Check compounds, flag undesirable groups, search for Baell's PAINS - Online
  • XLOGP3 - Compute logP - Online
  • MetaSite - Predict the site of metabolism for substrates of 2C9, 2D6, 3A4, 1A2 and 2C19 cytochromes - standalone, commercial
  • PharmGKB - A knowledge base that captures the relationships between drugs, diseases/phenotypes and genes involved in pharmacokinetics (PK) and pharmacodynamics (PD) - ADME/tox; PK/PD, online
  • CEBS - Chemical Effects in Biological Systems knowledge base (application of systems biology to ADME/Tox) - database
  • TissueTool - TissueDistributionDBs: A repository of tissue distribution profiles for identifying and ranking the genes in the spectrum of tissue specificity based on Expressed Sequence Tags (ESTs). This repository is currently available for several model organisms across animal and plant kingdoms and is fundamentally based on the UniGene database - Tissue distribution of several targets, online
  • Link - A KNIME workflow with Schrodinger tools to predict interactions with human serum albumin. Michelle Lynn Hall, William L Jorgensen, and Lewis Whitehead, J Chem Inf Model 2013. Automated ligand- and structure-based protocol for in silico prediction of HSA binding - serum albumin binding - HSA, online
  • Link - Evaluation of drug-human serum albumin binding interactions with support vector machine aided online automated docking. Bioinformatics 2011, Zsila et al - serum albumin binding - HSA, online
  • Link - Allows the users to predict whether a given compound is a P-gp substrate and how it binds to and interacts with P-gp - Pgp ADMET, online, commercial, allows one compound
  • SMARTCyp - Predicts the sites in molecules that are most liable to cytochrome P450 mediated metabolism - CYP450, online
  • IMPACTS - A program for the prediction of the sites of metabolism (SOM) of drugs in CYP P450 proteins based on docking and transition states - CYP450, standalone
  • Link - Ursu O, Oprea TI. J Chem Inf Model. 2010 Aug 23;50(8):1387-94. - drug-likeness, standalone
  • Link - Jim Empfield - physchem and drug - 2010 talk - Seminar
  • Link - Directory of computer-aided Drug Design tools - Drug Design tools
  • Pathguide - Contains information about 325 biological pathway related resources and molecular interaction related resources including Protein-Protein Interactions and many others - A pathway resource list
  • IUPHAR - the official database of the IUPHAR Committee on Receptor Nomenclature and Drug Classification. Incorporating detailed pharmacological, functional and pathophysiological information on G Protein-Coupled Receptors, Voltage-Gated Ion Channels, Ligand-Gated Ion Channels and Nuclear Hormone Receptors - database
  • PASS - PASS Inet predicts over 4000 kinds of biological activity, including pharmacological effects, mechanisms of action, toxic and adverse effects, interaction with metabolic enzymes and transporters, influence on gene expression, etc. - off-target, tox...online
  • Link - Modeling chemical mutagenicity. Langham JJ, Jain AN. J Chem Inf Model. 2008 48:1833-9. Contact the authors - ADMET-software, standalone
  • BOOMER - A Free GUI for BOOMER (BOOMER: an Excellent PK/PD Modeling Computer Program) - PK/PD standalone
  • Cyber Patient - A Multimedia Pharmacokinetic Simulation Program for Case Study Generation in a Problem-Solving Curriculum - PK/PD standalone
  • PKfit - A Data Analysis Tool for Pharmacokinetics - PK/PD standalone
  • JPKD - Formerly JavaPK for Desktop is a clinical pharmacokinetic (CPK) services (or therapeutic drug monitoring, TDM) computer program for desktop - PK/PD standalone
  • TDM - A R package for therapeutic drug monitoring - PK/PD standalone
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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira