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
  • REStLESS: Automated Translation of Glycan Sequences from Residue-Based Notation to SMILES and Atomic Coordinates
  • 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

  • GPCRdb 2018: adding GPCR structure models and ligands
  • WDL-RF :Predicting Bioactivities of Ligand Molecules Acting with G Protein-coupled Receptors by Combining Weighted Deep Learning and Random Forest
  • GPCR-SSFE :fragment-based molecular modeling web tool for Class A G-protein coupled receptors
  • Galaxy7TM :flexible GPCR-ligand docking by structure refinement (improves an input GPCR structure by simultaneous ligand docking and flexible structure refinement using GALAXY methods)
  • GPCR-ModSim :A comprehensive web based solution for modeling G-protein coupled receptors
  • ModRefiner :algorithm for atomic-level, high-resolution protein structure refinement
  • GPCR
  • GPCR-SSFE: including Snake-like-Plot for GPCRs
  • GPCRautomodel
  • GOMoDo

3D structure prediction for small compounds

Protein-protein docking (often online)

Protein-protein pairwise prediction & networks, pathways

Protein-protein binding region predictions

  • PROFisis
  • BIPSPI: a method for the prediction of Partner-Specific Protein-Protein Interfaces
  • ArDock: Identification and visualization of protein binding regions
  • ComplexContact (inter-protein contact prediction using deep learning)
  • DIBS (a repository of disordered binding sites mediating interactions with ordered proteins - database)
  • iPred scans the surface of a protein structure and identifies potential hotspots
  • IChemPIC Random forest classifier of biological and crystallographic protein-protein interfaces
  • SpotOn: Identification of Protein-Protein Interface Hot-Spots
  • metaPPI
  • PresCont
  • Cons-PPISP
  • bindML
  • Patch Finder
  • InterProSurf (analyze complexes)
  • Pred_PPI: sequences
  • PredUs
  • iFraG
  • PSC (protein surface classification)
  • PICI: identifying interaction sites within protein complexes
  • The database JET2 Viewer (putative protein binding sites, PPI, pocket descriptors, for all PDB structures)
  • ProteinPlus: structural analysis...
  • IBIS (Inferred Biomolecular Interaction Server)
  • PISA (PDBePISA, interactive tool for the exploration of macromolecular interfaces)
  • EPPIC: Evolutionary Protein-Protein Interface Classifier...
  • eFindSitePPI: detects protein binding sites (PPI)

Protein-protein complex prediction - template-based

Protein-membrane (transient or not) + interaction

Molecular simulation - refinement - flexibility (macromolecules)

  • Chiron minimizes steric clashes using short discrete molecular dynamics(DMD) simulations
  • Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Polarizable Force Fields
  • gRINN :a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations
  • MODE-TASK Large-scale protein motion tools
  • CABS-flex :fast simulations of flexibility of protein structures
  • Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques
  • Scoria: a Python module for manipulating 3D molecular data
  • HullRad Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties
  • DynaMine Fast predictor of protein backbone dynamics using only sequence information as input
  • QwikMD MD with VMD and NAMD (standalone Mac, Linux, Windows, Supercomputers)
  • WEBnm@ Web server and services for comparing protein flexibility
  • NMSim integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins
  • FoldX (simulation, Alascan, mutation, peptides...loops)
  • Naccess: calculates the accessible area of a molecule from a PDB file
  • FreeSASA: calculates the accessible area of molecules, different chains, etc
  • iFold for interactive protein folding/unfolding simulations
  • ProteinPrepare Make your protein ready for molecular dynamics simulations by titrating and protonating the protein at a desired pH and by optimizing the H-bond network
  • Adaptativesampling Explore the protein conformational space or protein-ligand interaction space by running MD simulations along the metric of your choice
  • PREFMD ( protein structure refinement via molecular dynamics simulations. Standalone scripts also available)
  • Abalone
  • AQUASOL predict water binding sites
  • VLDP can also be used to add water online
  • Princeton_TIGRESS
  • PreFRP
  • 3Drefine
  • ModRefiner
  • FG-MD
  • NOMAD-ref
  • iMODS
  • WEBnma
  • MDWeb
  • Gromacs
  • CHARMM-GUI (eg solvator to add water molecules...)
  • DynOmics (dynamics of structural proteome)
  • Amber tools
  • YASARA dynamics
  • FireProt: automated design of thermostable proteins
  • ReFOLD (Refinement of 3D protein models)
  • SEEKR (scripts for ligand-receptor kinetic calculations)
  • NWChem: High-Performance Computational Chemistry
  • MCTBI: metal ion effects in RNA structures
  • SimRNAweb (simulation RNA)
  • 3D-NuS (simulation non-canonical 3-Dimensional Nucleic Acid Structures)
  • FlexPred
  • Bio3D-web NMA: normal mode analysis of protein structures (elastic network models (ENMs), residue fluctuations, mode visualization...
  • LipidBuilder
  • HTMD

Electrostatics of macromolecules

  • Bluues
  • ProteinPrepare Make your protein ready for molecular dynamics simulations by titrating and protonating the protein at a desired pH and by optimizing the H-bond network
  • PBEQ Solver
  • PCE
  • H++
  • DelPhiPKa
  • DelPhiForce (electrostatic forces and energy calculations and visualization between two objects)
  • ESBRI (salt bridges, electrostatics)
  • SMPBS (size Modified Poisson-Boltzmann Solvers)
  • PDBparam (check salt-bridges, cation-pi, etc)

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 - Some can also be used for protein engineering

  • Genomic Position to Protein Sequence and 3D Structure at the PDB
  • VarAFT: disease-causing variants annotation
  • GDA :a web-based tool for Genomics and Drugs integrated analysis
  • SNPnexus :assessing the functional relevance of genetic variation to facilitate the promise of precision medicine
  • RFAmyloid: Server for Predicting Amyloid Proteins
  • DynaMut :predicting the impact of mutations on protein conformation, flexibility and stability
  • IMPACT : oncology database integrating molecular profiles with actionable therapeutics
  • KRDS a web server for evaluating drug resistance mutations in kinases by molecular docking
  • Variant Effect Predictor (VEP) VEP (Ensembl) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions
  • G2S A web-service for annotating genomic variants on 3D protein structures
  • Disulfide by Design 2.0 (DD2) (a web-based tool for disulfide engineering in proteins)
  • TANGO A computer algorithm for prediction of aggregating regions in unfolded polypeptide chains
  • FireProt: automated design of thermostable proteins
  • ADEPTUS discovery and analysis tool based on expression and mutation data from many diseases (eg., cancer)
  • Zebra a web server for bioinformatic analysis of diverse protein families
  • visualCMAT Helps to select and interpret correlated mutations/co-evolving residues in protein families
  • MAESTROweb :a web server for structure based protein stability prediction
  • Delta (DNA, Web-based 3D genome visualization and analysis platform)
  • SNPdryad (Deleterious Non-Synonymous SNP Predictions for Human, sequence)
  • pStab (Prediction of Stable Mutants (single- or multiple-point substitutions of charged residues, Unfolding Curves, Stability Maps and Protein Electrostatic Frustration)
  • Folding RaCe (method for predicting changes in protein folding rates upon point mutations (two-state folders))
  • ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures
  • nsSNPAnalyzer (predicting disease-associated nonsynonymous single nucleotide polymorphisms)
  • MutationTaster (sequence)
  • dSysMap (Mapping of Human disease-related mutations at the systemic level, structural interactome)
  • Hotspot3d (structure)
  • PISA (PDBePISA, interactive tool for the exploration of macromolecular interfaces)
  • SnpEff - SnpSift (Genetic variant annotation and effect prediction toolbox)
  • Auto-Mute 2.0 Sequence and structure based (stability change)
  • CScape : predicts oncogenic single-point mutations in the cancer genome
  • FATHMM-XF : accurate prediction of pathogenic point mutations via extended features
  • DUET: stability change by combining two approaches
  • CUPSAT Structure based (stability change)
  • Eris Structure based (stability change)
  • I-Mutant2.0 Sequence and structure based (stability change)
  • MuPro Sequence and structure based (stability change)
  • NeEMO Residue interaction networks (stability change)
  • PoPMuSiC 2.1 Structure based (stability change)
  • FATHMM Sequence based
  • MAPP Sequence based
  • Meta-SNP Consensus classifier
  • MuD Sequence and structure based
  • MutPred Sequence based
  • PANTHER-PSEP Sequence based
  • Parepro Sequence-based
  • PolyPhen-2 Sequence and (partially)-structure based
  • SIFT Sequence-based
  • SNAP Sequence-based
  • SNPs&GO Sequence and structure based
  • VAPOR (Variant Analysis Consensus classifier)
  • G23D
  • PredictSNP2 (consensus)
  • GenomeRunner
  • Cancer3D
  • mCSM-lig
  • Virtual Pharmacist
  • Plot protein: visualization of mutations
  • ESBRI (salt bridges, electrostatics)
  • PROVEAN (Sequence and structure based)
  • StructMAn
  • PsychoProt
  • Pharos (druggable genome - TCRD - (target central resource database))
  • BindProf (deltadeltaG on PPI interface, needs a list of residue)
  • DrugScorePPI (deltadeltaG on PPI interface) (systematic search, hotspots)
  • PredHS (protein-protein interaction hotspots (sort of deltadelta G)
  • Interpretome
  • dbSNP
  • 1000 genomes project
  • mutLBSgeneDB (mutated binding pockets)
  • Genomics, Evidence, Neoplasia, Information, Exchange (GENIE)
  • MSV3d
  • DaMold
  • INPS-MD (predict stability)
  • ABCMdb (mutations in ATP binding cassette proteins - ADMET)
  • Amino Acid Interaction (INTAA) - structural analysis
  • NewProt (protein engineering portal, mutation via HOPE & the Hotspot Wizard...)
  • PON-P2 predicts the pathogenicity of aa changes
  • VEST: Variant Effect Scoring Tool
  • MuPIT: map variant positions in 3D
  • CRAVAT: cancer-related analysis of variants toolkit
  • SODA (protein solubility)
  • FELLS (fast estimator of latent local structure)
  • DEOGEN2: predictor of missense SVNs
  • MutationAssessor
  • GenProBiS (mapping variants to protein binding sites)
  • mCSM-NA: (aa changes on protein-nucleic acids)
  • PhD-SNPg (coding and non-coding regions)
  • PMut
  • Prosat+ (protein structure annotation)
  • SIFTS (integrate 3D structure, function, taxonomy & sequence, PDB-UniProt mapping)
  • VCF.Filter (disease-linked genetic variants from sequencing data)
  • MAESTRO (multi agent stability prediction upon point mutations)
  • mCSM (effect of mutations on stability, PPI, protein-DNA)
  • SDM (impact of mutations on protein stability)
  • Protein-Sol (predict protein solubility from sequence)
  • Solubis (reduce protein aggregation through mutation, check for peptides)
  • AGGRESCAN3D (A3D): prediction of aggregation (proteins)
  • Protter (interactive protein feature visualization)
  • MutaGene (explore cancer mutations)
  • Variant Ranker (according to functional significance)
  • SCooP (protein stability curves as a function of the temperature, maybe not fully for point mutation but related)
  • MutaNET (analysis of genomic mutations in gene regulatory networks)
  • Spliceman2: predicts defects in pre-mRNA splicing

Peptide design

Structure-based virtual screening

Ligand-based virtual screening & de novo design


  • hERG
  • hERGdb: integrated database for hERG blocking small molecules
  • 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)
  • ADMETlab: Systematic ADMET evaluation based on a comprehensively collected ADMET database
  • HepatoPred-EL :prediction of chemical Hepatotoxicity using ensemble learning methods
  • CDPBC :A Software for Estimation of Concentration Dependent Plasma Binding Capacity of Small Molecule via docking
  • ToxPi: ToxPi Graphical User Interface 2.0: dynamic exploration, visualization, and sharing of integrated data models (standalone)
  • ChemoTyper: tool that allows for searching and highlighting chemical chemotypes (chemical substructures or subgraphs) in datasets of molecules. Can be used to search for structural alerts
  • eMolTox (174 predictions - off targets)
  • DDI predictor :a tool to optimize drug prescription (A tool to optimize drug prescription - CYP)
  • MetStabOn :metabolic stability predictions (predict t1/2 of compounds)
  • CLC-Pred :in silico prediction of human cell line cytotoxicity
  • OPERA :OPEn (q)saR App (models for predicting physicochemical preperties and environmental fate endpoints)
  • cBinderDB :a covalent binding agent database
  • CompTox Chemistry Dashboard :a community data resource for environmental chemistry
  • Hit Dexter :Machine-learning Model for the Prediction of Frequent Hitters
  • vNN: Web Server for ADMET Predictions
  • ADVERPred :prediction of adverse effects of drugs (use black box warning...)
  • ADReCS-Target : The Adverse Drug Reaction Classification System-Target Profile provides comprehensive information about ADRs caused by drug interaction with protein, gene and genetic variation
  • NPASS :natural product activity and species source database
  • MouseTox :cytotoxicity assessment for small molecules
  • ROSC-Pred :rodent organ-specific carcinogenicity prediction
  • 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, predict aqueous solubility, deep learning)
  • 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
  • ProTox-II : a webserver for the prediction of toxicity of chemicals
  • 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-Drugs4 or Tripod
  • 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, drug combination

Other directories of tools

"Data manipulation tools - learning - descriptors - model repository"

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