Examples of tools extracted from the various sections

If VLS3D is useful for your research
Please cite: Villoutreix et al. Drug Discovery Today 2013, 18:1081-9



2D molecular visualization (chemicals & proteins)

Some protein sequence tools (online 3D or 2D)

3D molecular visualization

3D structure prediction and validation : macromolecules
Homology Modeling & others

Glycomics, carbohydrates and glycobiology research

  • GLYCAM-Web: 3D prediction of carbohydrates and proteins-carbohydrates
  • UniCarbKB: online information storage and search platform for glycomics, carbohydrates and glycobiology research
  • databases and bioinformatics tools for glycobiology, carbohydrates and glycomics
  • Glyco3D: a portal for structural glycosciences, glycobiology, carbohydrates

Antibody modeling & related

GPCR modeling

3D structure prediction for small compounds

Protein-protein docking (online)

Protein-protein pairwise prediction & networks, pathways

Protein-protein binding region predictions

Protein-protein complex prediction - template-based

Protein-membrane (transient or not) + interaction

Molecular simulation - refinement - flexibility (macromolecules)

Electrostatics of macromolecules

Ligand-binding pockets

Biostructural pathology / Structural analysis

Amino acid changes in the 3D structures can be introduced with PyMOL, Chimera, or online with PDB_HYDRO, used for adding water, to mutate...

Variation databases

Some tools to analyze variants

Peptide design

Structure-based virtual screening

Ligand-based virtual screening & de novo design


  • hERG
  • VirtualToxLab :3D ADMET, hERG, CYP...
  • LimTox : text mining adverse event and toxicity associations of compounds, drugs and genes
  • FAME2 Effective Machine Learning Model of Cytochrome P450 Regioselectivity
  • Pred-hERG
  • Pred-Skin :chemically-induced skin sensitization
  • FDALabel
  • DrugBank
  • DrugCentral
  • AquaSolWeb (UG-RNN)
  • XenoSite (metabolism P450)
  • MLViS (can classify molecules as drug-like and nondrug-like based on various machine learning methods)
  • ADME SARfari : Predict likely ADME targets for an input molecule
  • DruLiTo : Predict drug-likeness of a compound (RO5, MDDR rules, Veber rules, Ghose, BBB rule, CMC-50 rule, QED)
  • PROTOX : a webserver for the prediction of oral toxicities of small molecules in rodents
  • Alkemio : Association of chemicals with biomedical topics by text and data mining
  • PAINS-Remover: PAINS compounds
  • ACD/I-Lab : ADME, physchem
  • SwissADME : Compute physicochemical descriptors as well as predict pharmacokinetics properties and druglike nature of one or multiple small molecules (BBB, Cyp, Pgp...)
  • Solubility via OCHEM (also structural alerts, plasma binding, BBB...CYP, AMES..) optimization of compounds via cmpd matched pairs, MolOptimiser)
  • Eli Lilly Open Innovation (medchem: structural alerts and drug-likeness) online via FAF-Drugs3 or Tripod
  • FAF-Drugs4: PAINS, Veber, rule of 5, ppiHit profiler, 3/75, structural alerts, oral, phospholipidosis... traffic light... (it prepares cmpd collections and helps select molecules for optimization, remove duplicate, draw a compound and analysis...and FAF-QED)
  • Eli Lilly medchem rules implemented at Tripod
  • 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
  • WhichCyp Web Service (WhichCyp predicts which P450 isoform will bind/metabolize a molecule using simple yes/no classification models)
  • Metabolic site predictor: MetaPrint2D-React
  • Aggregator Advisor
  • Pains and aggretators via Zinc
  • ToxCreate (Acute dermal toxicity, Acute oral toxicity, Blood-brain barrier penetration, Carcinogenicity, DNA-binding, Eye irritation/corrosion, Mutagenicity)
  • The HExpoChem server contains information on diverse sources of chemicals with the aim to explore human health risk from chemical exposure
  • QED, quantitative estimation of drug-likeness
  • DrugMint is a web server developed for predicting drug-likelihood of a compound
  • SOMEViz (Site of Metabolism Estimator Visualization)
  • Mcule property calculator
  • RS-WebPredictor: Predict cytochrome P450-mediated sites of metabolism on drug-like molecules
  • DemQSAR Online Human Volume of Distribution and Human Clearance
  • ChemBioServer: Toxicity Filtering (some Toxicophores)
  • BBB predictor
  • ADME calculator (Druglikeness, logS, GenoToxicity, pKa)
  • OSIRIS Property Explorer
  • Toxtree online (not sure it still works)
  • DrugLogit Calculators (druglikeness)
  • SmartsFilter (many structural alerts and PAINS)
  • PharmGKB is a comprehensive resource that curates knowledge about the impact of genetic variation on drug response for clinicians and researchers
  • Interaction (site 1, 2 and 3) with Serum albumin
  • SMARTCyp Predicts the sites in molecules that are most liable to cytochrome P450 mediated metabolism
  • CypRules: A rule-based P450 inhibition prediction server (2015, the standalone is also available)
  • LTMap: a web server for assessing the potential liver toxicity by genome-wide transcriptional expression data (2014)
  • pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures
  • SCYPPred: A web-based predictor of SNPs for human cytochrome P450 (2012)
  • PASS online
  • admetSAR webserver (at LMMD, many endpoints, hERG, Cyp, other tox, plasma binding...)
  • Construction and analysis of a human hepatotoxicity database suitable for QSAR modeling using post-market safety data (model to do, see the reference)
  • Transformer (biotransformation of xenobiotics)
  • DailyMed provides high quality information about marketed drugs
  • The BioZyne P-gp server uses a Support Vector Machine classifier
    to predict whether a compound is likely to be a substrate of the P-gp drug efflux pump
  • BADAPPLE (related to PAINS, search for promiscuous cmpds)
  • Molinspiration (physchem, bioactivity predictions on kinases, ion channels, enzyme, nuclear receptors, GPCR, proteases)
  • SOMP is a web-service for in silico prediction of site of metabolism (SOM) (CYPs)
  • SOM prediction (CYPs)
  • QTdrugs (torsadogenic risk) lists
  • Statistical data mining of Adverse Event Reporting System (AERS Spider)
    is a public online analytical tool which is based on publicly available AERS data
  • hERGCentral
  • CompTox Dashboard (EPA)
  • Some web servers for the prediction of drug–drug interactions (DDI)
  • SuperCYP A collection of CYP enzymes and a tool to analyze cytochrome P450-mediated DDI
  • whichCyp: Predicts inhibition of P450 enzymes using machine learning approaches
  • P-gp substrate prediction using SVM and docking (Pgp)
  • P-gp substrate and inhibitor classification using SVM model, rule-based models, and effluxophore detection (Pgp)
  • BCRP Human breast cancer resistance protein (BCRP) is an ATP-binding cassette (ABC) efflux transporter that confers multidrug resistance in cancers,
    and also plays an important role in the absorption, distribution and elimination of drugs. The server allows the users to predict whether a query compound is a wild-type BCRP substrate
  • INDI Informatics-based prediction on CYP-related PK DDI (Inferring novel drug-drug interactions)
  • DDI-CPI Web tool for DDI prediction using molecular docking (needs login)
  • Human Intestinal Transporter Database QSAR models to predict drug interactions mediated by transporters - Accessed through Chembench
  • MetaPrint2D Predicts site of metabolism
  • admetSAR A large number of ADME/Tox QSAR models
  • OCHEM Many ADME/Tox QSAR models
  • Virtual Pharmacist
  • UCSF-FDA TransPortal
  • DILI Deep Learning for Drug-Induced Liver Injury (DILIserver)
  • Metabolic stability -Half life (CACTUS)
  • Gusar antitargets, rat toxicity...
  • CoFFer (76 QSAR models, off-targets..)
  • Connection Map for Compounds (CMC)
  • e-Drug3D-PK: Structure-Pharmacokinetic Parameters Data Set
  • Dark chemical matter datasets (supplement data, interesting for PAINS...etc)
  • CIPA (hERG cmpds database)
  • Drug-Induced Liver Injury Network (Dilin)
  • Endocrine Disruptome
  • Metatox (predict metabolites and toxicity of metabolites, way2drug)
  • hERGscreen (3D pharmacophore models, natural products)
  • CarcinoPred-EL (carcinogenicity of chemicals)
  • Drug Interaction Database (commercial)
  • TOXNET Databases
  • The eTOX project (develops a drug safety database)
  • (ADME gene list)
  • Drug Interaction Database - DIDB (metabolism & transport)
  • Open TG-GATEs (toxicogenomics)
  • Pharmacogenetics Database (e-PKGene)
  • JAPIC (side effects)
  • Look at your compounds with standalone tools:
    DataWarrior, ...ICM chemistry,.. Many tools are also included in the Chemaxon packages

Compound collections, medicinal drugs & pharmacology/protein databases

Repositioning, repurposing,
polypharmacology, target fishing

Other links directories

"Data manipulation tools - learning - model repository"

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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira