Web services

• TarFisDock. Web server for identifying drug targets with docking approach. The server is freely accessible for anonymous user. Docks small molecules into the protein targets in PDTD (Potential Drug Target Database), and outputs the top candidates ranked by the energy score, including their binding conformations and a table of the related target information.
  
• SEA. (Similarity ensemble approach) relates proteins based on the set-wise chemical similarity among their ligands. It can be used to rapidly search large compound databases and to build cross-target similarity maps. Provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF).
  

Web services

• 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.
  

Software

• 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.
  
• ACD/Structure Design Suite. Helps chemists optimize the physicochemical properties of their compounds. The software suggests alternative substituents (at a site/sites on the molecule) to drive the property of choice in the desired direction. Helps adjust aqueous solubility, lipophilicity (logP or logD), or change the ionization profile (pKa) of molecules. Distributed by ACD/Labs.
  

Software

• cQSAR. A regression program that has dual databases of over 21,000 QSAR models. Distributed by BioByte.
  
• clogP. Program for calculating log P_oct/water from structure. Distributed by BioByte.
  
• ClogP/CMR. Estimates Molar Refractivity and logP. Distributed by Tripos.
  

Web services

• XScore-LogP. Calculates the octanol/water partition coefficient for a drug, based on a feature of the X-Score program.
  

Software

• 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.
  
• Filter-it. Command-line program for filtering molecules with unwanted properties out of a set of molecules. The program comes with a number of pre-programmed molecular properties that can be used for filtering. Open source software distributed by Silicos.
  
• Virtual LogP. Bernard Testa's Virtual logP calculator. Provided by the Drug Design Laboratory of the University of Milano.
  
• 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.
  
• ADRIANA.Code. Program to calculate physico-chemical properties of small molecules: number of H-bonds donor and acceptors, logP, logS, TPSA, dipole moment, polarizability, etc. Distributed by Molecular Networks.
  
• Derek Nexus. Predicts toxicity properties using QSAR and other expert knowledge rules. Distributed by Lhasa Limited.
  
• Meteor. Predicts metabolic fate of chemicals using other expert knowledge rules in metabloism. Distributed by Lhasa Limited.
  
• 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.
  
• pKalc. Program for predicting acidic and basic pKa. 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.
  
• ToxTree. Full-featured and flexible user-friendly open source application to estimate toxic hazard by applying a decision tree approach. Provided by IdeaConsult Ltd.
  
• 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.
  
• SMARTCyp. SMARTCyp predicts the sites in molecules that are most liable to cytochrome P450 mediated metabolism. For Windows, Mac and Linux. Provided under the GPL license by the the Department of Medicinal Chemistry at the University of Copenhagen.
  
• StarDrop. Allows the identification of the region of a molecule that are the most vulnerable to metabolism by the major drug metabolising isoforms of cytochrome P450. Distributed by optibrium.
  
• isoCYP. Software for the prediction of the predominant human cytochrome P450 isoform by which a given chemical compound is metabolized in phase I. Distributed by Molecular Networks.
  

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.
  
• 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 all rules is available. Maintained by the University of Minnesota.
  
• 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. Maintained by the University of Singapore.
  
• 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.
  
• Lazar. Lazy Structure Activity Relationships. Derives predictions from toxicity databases by searching for similar compounds. provided free of charge by in silico toxicology.
  
• 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.
  
• SMARTCyp Web Service. SMARTCyp predicts the sites in molecules that are most liable to cytochrome P450 mediated metabolism. Provided by the the Department of Medicinal Chemistry at the University of Copenhagen.
  

Databases

• TOXNET. Databases on toxicology, hazardous chemicals, environmental health, and toxic releases that can be accessed using a common search interface. provided by the Unied States NLM.
  
• Leadscope Toxicity Database. Database of 160,000 chemical structures with toxicity data. Distributed by Leadscope.
  
• Cloe Knowledge. Open Access ADME/PK Database for a range of marketed drugs. Maintained by Cyprotex.
  
• PHYSPROP. The Physical Properties Database (PHYSPROP) contains chemical structures, names, and physical properties for over 41,000 chemicals. Physical properties are collected from a wide variety of sources, and include experimental, extrapolated, and estimated values for melting point, boiling point, water solubility, octanol-water partition coefficient, vapor pressure, pKa, Henry's Law Constant, and OH rate constant in the atmosphere. Maintained by SRC.
  
• 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 332828 drug-target relations.
  
• ACToR. Database of all publicly available chemical toxicity data that can be used to find potential chemical risks to human health and the environment. ACToR aggregates data from over 500 public sources on over 500,000 environmental chemicals searchable by chemical name, other identifiers and by chemical structure. Provided by the EPA (USA Environmental protection Agency).
  
• DART. (Drug Adverse Reaction Target). A database for facilitating the search for drug adverse reaction target. It contains information about known drug adverse rection targets, functions and properties. Associated references are also included. Maintained by the University of Singapore.
  
• DITOP. (Drug-Induced Toxicity Related Proteins). Database of proteins that mediate toxicities through their interaction with drugs or reactive metabolites. Can be searched using keywords of chemicals, proteins, or toxicity terms. Maintained by the Xiamen university.
  
• ADMEAP. 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. Associated references are also included. Currently this database contains 321 protein entries. Maintained by the Dept.Computational Science. NUS.
  
• 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.
  
• HMDB. The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. The database contains chemical data, clinical data, and molecular biology/biochemistry data. The database (version 2.5) contains over 7900 metabolite entries including both water-soluble and lipid soluble metabolites as well as metabolites that would be regarded as either abundant (> 1 uM) or relatively rare (< 1 nM). Provided by the Departments of Computing Science & Biological Sciences, University of Alberta.
  
• t3db. (Toxin and Toxin Target Database). Combines detailed toxin data with comprehensive toxin target information. The database currently houses over 2900 toxins described by over 34 200 synonyms, including pollutants, pesticides, drugs, and food toxins, which are linked to over 1300 corresponding toxin target records. Altogether there are over 33 800 toxin, toxin target associations. Each toxin record (ToxCard) contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information. This information has been extracted from over 5600 sources, which include other databases, government documents, books, and scientific literature. Provided by the Departments of Computing Science & Biological Sciences, University of Alberta.
  
• SuperToxic. Collection of toxic compounds from literature and web sources. The current version of this database compiles approx. 60,000 compounds with about 100,000 synonyms. These molecules are classified according to their toxicity based on more than 2,500,000 measurements. Provided by Charité Berlin, Structural Bioinformatics Group.
  
• SuperHapten. Comprehensive database for small immunogenic compounds. Contains currently 7257 haptens, 453 commercially available related antibodies and 24 carriers. Provided by Charité Berlin, Institute of Molecular Biology and Bioinformatics.
  
• HaptenDB. Database of about 1087 haptens that includes common and chemical name of Hapten, molecular mass, physical and chemical properties, biological importance and the structure. Provided by the Institute of Microbial Technology, India.
  
• SuperCyp. Comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Provided by Charité Berlin, Structural Bioinformatics Group.
  
• PROMISCUOUS. Exhaustive resource of protein-protein and drug-protein interactions with the aim of providing a uniform data set for drug repositioning and further analysis. PROMISCUOUS contains three different types of entities: drugs, proteins and side-effects as well as relations between them. Provided by Charité Berlin, Structural Bioinformatics Group.