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Thursday, October 20, 2011

[+] Databases

Zinc Database, ChEMBL, CoCoCo, Protein DataBank (PDB), Binding MOAD (Mother Of All Database), Ligand Protein DataBase (LPDB), TTD, ...

[+] Chemical structure representations

ChemDraw, MarvinSketch, ACD/ChemSketch, ChemWriter, jsMolEditor, Marvin molecule editor and viewer, UCSF Chimera, Pymol, Swiss-PDB Viewer / DeepView, Daylight SMILES, InChI, Tripos Mol2, OpenBabel, LigPrep, Corina, PoseView, DS Visualizer, E-Babel, Corina online demo, Chemical Identifier Resolver, ChemMobi, ...

[+] Molecular Modeling

CHARMM, GROMACS, Amber, SwissParam, CHARMMing.org, Dundee PRODRG2 Server, ...

[+] Homology Modeling

Modeller, I-TASSER, ProModel, SWISS-MODEL, SWISS-MODEL Repository, ModBase, ...

[+] Binding site prediction

MED-SuMo, CAVER, FINDSITE, sc-PDB, CASTp, Pocketome, 3DLigandSite, metaPocket, PASS, ...

[+] Docking

Autodock, DOCK, GOLD, SwissDock, DockingServer, Blaster, ...

[+] Screening

CoLibri, Corina, Pharmer, Blaster, FINDSITE-LHM, e-LEA3D, ...

[+] Ligand design

GANDI, FlexNovo, BREED, Glide Fragment Library, e-LEA3D, 3DLigandSite, PASS, ...

[+] Binding free energy estimation

X-score, DrugScoreONLINE, BAPPL server, BAPPL-Z server, ...

[+] QSAR

cQSAR, clogP, ClogP/CMR, MOLE db, ChemDB/Datasets, Datasets from the Milano Chemometrics and QSAR Research Group, MolInfo, E-Dragon, Pattern Match Counter, ...

[-] ADME Toxicity

QikProp, q-ADME, q-TOX, ALOGPS, OSIRIS Property Explorer, ToxPredict, PK/DB, Leadscope Toxicity Database, The ADME databases, ...


  • QikProp. Provides rapid ADME predictions of drug candidates. Distributed by Schrodinger.
  • q-ADME. Predicts the following properties: Drug half-life (T1/2); Fraction of oral dose absorbed (FA); Caco-2 permeability; Volume of distribution (VD); Octanol/water distribution coefficient (LogP).
  • q-TOX. Computes toxic effects of chemicals solely from their molecular structure (LD50, MRDD, side effects).
  • VolSurf. Calculate ADME Properties and Create Predictive ADME Models. Distributed by Tripos.
  • Metabolizer Preview. Enumerates all the possible metabolites of a given substrate, predicts the major metabolites and estimates metabolic stability. It can be used for the identification of metabolites by MS mass values, discovery of metabolically sensitive functionalities and toxicity prediction, and provide information related to the environmental effects of chemicals by bacterial degradation. Provided by ChemAxon.
  • ACD/PhysChem Suite. Predicts basic physicochemical properties, like pKa, logP, logD, aqueous solubility and other molecular properties in seconds, usr a fragment-based models. Distributed by ACD/Labs.
  • ACD/ADME Suite. Predicts of ADME properties from chemical structure, like Predict P-gp specificity, oral bioavailability, passive absorption, blood brain barrier permeation, distribution, P450 inhibitors, substrates and inhibitors, maximum recommended daily dose, Abraham-type (Absolv) solvation parameters. Distributed by ACD/Labs.
  • ACD/Tox Suite. Collection of software modules that predict probabilities for basic toxicity endpoints. Several modules including hERG Inhibition, CYP3A4 Inhibition, Genotoxicity, Acute Toxicity, Aquatic Toxicity, Eye/Skin Irritation, Endocrine System Disruption, and Health Effects. Distributed by ACD/Labs.
  • ACD/DMSO Solubility. Predicts solubility in DMSO solution. Distributed by ACD/Labs.
  • Sieve. Program for filtering out molecules with unwanted properties. Open source software distributed by Silicos.
  • ONTOMINE. Fingerprints-based data mining software used for automated Molecular Mining for BioActivity, Toxicity and Side effect prediction.
  • FAF-Drugs2. Free package for in silico ADMET filtering. Distributed by the university of Paris Diderot.
  • ADMET Predictor. Software for advanced predictive modeling of ADMET properties. Distributed by Simulations plus, Inc.
  • ClassPharmer. ClassPharmer is a cheminformatics platform for lead identification and prioritization, de novo design, scaffold hopping and lead optimization. The software is divided into four modules – Basic, SAR, Design and ADMET – each of which can be licensed separately. Distributed plu Simulation Plus, Inc.
  • GastroPlus. Simulates the oral absorption, pharmacokinetics, and pharmacodynamics for drugs in human and preclinical species. The underlying model is the Advanced Compartmental Absorption and Transit (ACAT) model. Distributed plu Simulation Plus, Inc.
  • Discovery Studio TOPKAT Software. Cross-validated models for the assessments of chemical toxicity from chemical's molecular structure. Distributed by Accelrys.
  • Discovery Studio ADMET Software. The ADMET Collection provides components that calculate predicted absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties for collections of molecules. Distributed by Accelrys.
  • PreADME. Calculates molecular descriptors. Predicts Drug-likeness. ADME predictions.
  • Molcode Toolbox. Molcode Toolbox allows prediction of medicinal and toxicological endpoints for a large variety of chemical structures, using proprietary QSAR models.
  • KOWWIN - EPI Suite. Estimates the log octanol-water partition coefficient of chemicals using an atom/fragment contribution method. Distributed by the EPA~s Office of Pollution Prevention Toxics and Syracuse Research Corporation (SRC) as part of the EPI Suite. For Windows.
  • ChemTree. Predicts ADME/Tox properties using QSAR. Distributed by Golden Helix.
  • OncoLogic. Evaluates the likelihood that a chemical may cause cancer, using SAR analysis, experts decision mimicking and knowledge of how chemicals cause cancer in animals and humans. Distributed for free by the US Environmental Protection Agency (EPA).
  • HazardExpert Pro. Predicts the toxicity of organic compounds based on toxic fragments. Distributed by CompuDrug.
  • MetabolExpert. Predicts the most common metabolic pathways in animals, plants or through photodegradation. Distributed by CompuDrug.
  • MEXAlert. Identifies compounds that have a high probability of being eliminated from the body in a first pass through the liver and kidney. Distributed by CompuDrug.
  • PrologP/PrologD. Predicts the logP/logD values using a combination of linear and neural network methods. Distributed by CompuDrug.
  • Leadscope. Estimates toxiticy using QSAR. Distributed by Leadscope.
  • COMPACT. Identifies potential carcinogenicity or toxicities mediated by CYP450s.
  • CASETOX. Uses MCASE to predict toxicity. Distributed by MultiCASE.
  • META. Predicts metabolic paths of molecules. Distributed by MultiCASE.
  • PK-Sim. Predicts ADMET properties. Distributed by Bayer technology Services.
  • SimCYP. The SimCYP Population-based ADME Simulator is a platform for the prediction of drug-drug interactions and pharmacokinetic outcomes in clinical populations. Distributed by SimCYP.
  • Cloe Predict. Pharmacokinetic prediction using phisiologically based pharmacokinetic modeling (PBPK), and prediction of human intestinal absorption using solubility, pKa and Caco-2 permeability data. Distributed by Cyprotex Discovery.
  • KnowItAll - ADME | Tox Edition. Prediction of ADME Tox properties using consensus modeling. Distributed by Bio-Rad Laboratories.
  • PASS. Identification of probable targets and mechanisms of toxicity.
  • MetaDrug. Predicts toxicity and metabolism of compounds using >70 QSAR models for ADME/Tox properties. Distributed by GeneGo.
  • ADMEWORKS ModelBuilder. Builds QSAR/QSPR models that can later be used for predicting various chemical and biological properties of compounds. Models are based on values of physicochemical, topological, geometrical, and electronic properties derived from the molecular structure, and can be imported into ADMEWORKS Predictor.
  • ADMEWORKS Predictor. Virtual (in silico) screening system intended for simultaneous evaluation of the ADMET properties of compounds. It complements existing in silico technologies for evaluating pharmacological properties.
  • MetaSite. Computational procedure that predicts metabolic transformations related to cytochrome-mediated reactions in phase I metabolism. The method predicts "hot spots" in the molecule, suggests the regions that contribute most towards each "hot spot", providing additional derivation sites for chemists to design new stable compounds, predicts the structures of the most likely metabolites and warns about the potential of CYP mechanism-based inhibition. Distributed by Moldiscovery.

Web services

  • ALOGPS. On-line prediction of logP, water solubility and pKa(s) of compounds for drug design (ADME/T and HTS) and environmental chemistry studies. ALOGPS also displays values calculated with Pharma Algorithms LogP, LogS and pKa, Actelion LogP & LogS (many thanks to Dr Thomas Sander), Molinspiration logP, KOWWIN logP, ALOGP (Viswanadhan et al, 1989), MLOGP (Moriguchi et al, 1992) implemented in the DragonX software, XLOGP2 and XLOGP3 programs and ChemAxon logP calculator
  • OSIRIS Property Explorer. Integral part of Actelion's inhouse substance registration system. Calculates on-the-fly various drug-relevant properties for drawn chemical structures, including some toxicity and druglikeness properties. Maintained by the Virtual Computational Chemistry Laboratory.
  • ToxPredict. 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. Provided by OpenTox.
  • ToxCreate. Web service to create computational models to predict toxicity. Provided by OpenTox.
  • ADME-Tox. ADME-Tox (poor absorption, distribution, metabolism, elimination (ADME) or toxicity) filtering for small compounds, based on a set of elementary rules.
  • STITCH. Resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. STITCH contains interactions for over 74,000 small molecules and over 2.5 million proteins in 630 organisms.
  • XScore-LogP. Calculates the octanol/water partition coefficient for a drug, based on a feature of the X-Score program.
  • VirtualToxLab. ''In silico'' tool for predicting the toxic (endocrine-disrupting) potential of existing and hypothetical compounds (drugs, chemicals, natural products) by simulating and quantifying their interactions towards a series of proteins known to trigger adverse effects using automated, flexible docking combined with multi-dimensional QSAR (mQSAR).
  • PharmMapper. Freely accessed web-server designed to identify potential target candidates for the given probe small molecules (drugs, natural products, or other newly discovered compounds with binding targets unidentified) using pharmacophore mapping approach.
  • MODEL - Molecular Descriptor Lab. Computes structural and physichemical properties of molecules from their 3D structures.
  • PreADMET. Web-based application for predicting ADME data and building drug-like library using in silico method.
  • Free ADME Tools. ADME Prediction Toolbox of the SimCYP application provided free of charge by SimCYP.
  • UM-BBD Pathway Prediction System. The PPS predicts 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. Provided by the University of Minnesota.
  • MetaPrint2D. Metabolic site predictor. MetaPrint2D is a tool that predicts xenobiotic metabolism through data-mining and statistical analysis of known metabolic transformations reported in scientific literature. MetaPrint2D-React can make predictions concerning a wider range of reactions than MetaPrint2D, and is able to predict the types of transformation that can take place at each site of metabolism, and the likely metabolite formed. Provided by the University of Cambridge.
  • MetaPrint2D-React.. Metabolic site predictor. MetaPrint2D is a tool that predicts xenobiotic metabolism through data-mining and statistical analysis of known metabolic transformations reported in scientific literature. MetaPrint2D, which predicts sites of phase I metabolism, defined as the addition of oxygen (e.g. hydroxylation, oxidation, epoxidation) or elimination reactions. Provided by the University of Cambridge.


  • PK/DB. Freely available database for pharmacokinetic properties, designed with the aim of creating robust databases for pharmacokinetic studies and in silico ADME (Absorption, Distribution, Metabolism, and Excretion) prediction.
  • Leadscope Toxicity Database. Database of 160,000 chemical structures with toxicity data. Distributed by Leadscope.
  • The ADME databases. Databases for benchmarking the results of experiments, validating the accuracy of existing ADME predictive models, and building new predictive models.
  • The ADME database. Provides comprehensive data for structurally diverse compounds associated with known ADME properties, including human oral bioavailability, enzymes metabolism, inhibition and induction, transport, plasma protein binding and bloodbrain barrier. Distributed by Aureus.
  • SuperTarget Database. Database of about 7300 drug-target relations.
  • SIDER. (Side Effect Resource). contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drug–target relations.
  • ADME DB. Database containing data on interactions of substances with Drug Metabolizing Enzymes and Drug Transporters. It is designed for use in drug research and development, including drug-drug interactions and ADME (Absorption, Distribution, Metabolism and Excretion) studies.
  • SAR Genetox Database. Genetic toxicity database to be used as a resource for developing predictive modeling training sets. Distributed by Leadscope.
  • SAR Carcinogenicity Database. Carcinogenicity database with validated structures to be used as a resource for preparing training sets. Distributed by Leadscope.

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