Links to various (Q)SAR tools
Many (Q)SAR tools and databases are freely available on the internet. The following text presents a brief description and links to some of the systems that are most frequently used in connection with the work relating to chemical regulation.
AMBIT XT was developed by the chemical industry. Among other things, the database contains various models for PBT (persistent, bioaccumulable, toxic) assessment, identification of structural analogues and the building of chemical categories. The system contains both (Q)SAR predictions and test data.
AMBIT XT can be found via the following link: http://ambit.sourceforge.net/intro.html
CAESAR consists of a group of (Q)SAR models that were specially developed with a view to use under REACH. The project, which was financed by the EU, has developed models for bioconcentration factor (BCF), skin allergy, cancer, mutagenicity (the capacity to induce genetic mutation) and reproductive toxicity (impairment of fertility and normal development, including foetal damage).
See the CAESAR project's website: http://www.caesar-project.eu/software/index.php
The Danish (Q)SAR Database
The Danish (Q)SAR Database was developed by a group of researchers from Food DTU - the National Food Institute with support from a number of organisations including the Danish Environmental Protection Agency. The database contains estimates for more than 170,000 organic substances from more than 70 different (Q)SAR models.
The database also contains predictions for a wide variety of human-toxicological effects and for toxicity with respect to organisms, which are used to assess effects in the environment.
The Danish (Q)SAR Database was published in 2004 and is freely available on the internet. In the database, users can search for the modelled effects/properties of a specific substance.
See the Danish (Q)SAR Database
The Advisory List for Self-classification
Predictions from the Danish (Q)SAR database have been used to derive advisory self-classifications for over 30,000 substances. The list of self-classifications and background documentation can be found on the Danish Environmental Protection Agency website:
The Advisory List for Self-classification of Dangerous Substances.
EPISUITE is a collective term for a group of (Q)SAR models developed by the United States Environmental Protection Agency (US EPA). The package includes models that can predict physico-chemical properties such as log Kow (KOWWIN), water solubility (WSKOW), Henry's law constant (HenryWin), etc. It also contains models that can predict the fate of organic substances in the environment, including bioaccumulation potential (BCFBAF), biodegradability (BioWin) and hydrolysis rate (HydroWin). Finally, the database contains models that can predict the toxicity of organic substances with respect to aquatic organisms (Ecosar).
EPISUITE is a free program and can be downloaded from the US EPA's website. On this website, you will also find more information on the program and the models:
(Q)SAR models for toxicity with respect to fish, human liver toxicity, mutagenicity and cancer, etc. The software program also indicates the 10 closest neighbours (the 10 chemicals in the training set which most closely resemble the chemical being investigated).
The NCI database, which was developed by the US National Center for Cancer Research, contains (Q)SAR predictions for many different biological activities. These can for example be used to investigate the mechanisms of action of various types for chemical substances (including mechanisms of action in connection with the development of cancer).
The NCI database: http://cactus.nci.nih.gov/ncidb2.2/
OECD (Q)SAR Application Toolbox
The OECD has sponsored the development of the expert system "OECD (Q)SAR Application Toolbox". This program can be used to group chemicals into categories and to facilitate a better mechanistic understanding of a given effect. The OECD (Q)SAR Toolbox also enables users to develop their own (Q)SAR models. In addition, the system contains a large amount of test data, enabling it to be used to identify test data and to fill in gaps with read-across and (Q)SAR modelling where insufficient test data is available for a given chemical.
The OECD (Q)SAR Toolbox also contains the predictions from the Danish (Q)SAR Database.
The program can be downloaded free of charge from the OECD website:
OECD (Q)SAR Application Toolbox
PBT profiler have been developed by the United States Environmental Protection Agency (US EPA) with the aim of identifying possible PBT substances (substances that are persistent, bioaccumulable and toxic) where insufficient test data is available. This program combines predictions of a chemical's degradation, bioaccumulation (BCF) and toxicity with estimates of the chemical's distribution in the environment. PBT profiles use (Q)SAR predictions from EPISUITE, which are compared with US cut-off limits in relation to PBT criteria.
The programme is available free of charge online: http://www.pbtprofiler.net/
SPARC is a free online tool that can provide estimates of physical/chemical properties, including certain properties that are not covered by the EPIWIN models (e.g. log D).
Toxtree is a decision-making tree where so-called "structural alerts" (fragments of the molecule that are known to be associated with a particular effect, e.g. mutagenicity) are used to subdivide chemicals into different classes. Toxtree can be downloaded from the European Chemicals Bureau (ECB) website:
Many commercial models are available which require payment from the user prior to use. However, many of these systems can be used to a limited extent free of charge. Examples of commercial (Q)SAR systems are: ACD/Tox Suite, MultiCASE, MDL QSAR, LEADSCOPE, TOPKAT, DEREK for Windows, CATABOL, METEOR, META, Simulation Plus.