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Toxmatch

Contact: Nina Jeliazkova

Categories: Prediction, Data access

Exposed methods:

Description:

Toxmatch 1.05 (Java, GPL)
Provides means to compare a chemical or set of chemicals to a toxicity dataset through the use of similarity indices
Intended use is one to many or many to many quantitative read-across
To help in the systematic formation of groups and read-across
emphasis on endpoint-dependent similarity
Includes datasets for four toxicity endpoints to facilitate endpoint specific read-across

The aquatic toxicity dataset is a copy of DSSTox EPA Fathead Minnow Acute Toxicity dataset (April 2006 update) containing 617 chemicals
The bioconcentration factor dataset comprises LogBCF values for 610 non-ionic chemicals

  1. The skin sensitisation dataset contains local lymph node assay (LLNA) data for 210 chemicals, as published by Gerberick et al (2005)
  2. A qualitative classification of potency category and reaction domain is also reported for each compound, where potency category is one of non-sensitiser, weak sensitiser, moderate sensitiser, strong sensitiser, extreme sensitiser (as defined by Kimber et al., 2003) and reaction domain is one of Michael acceptors (MA), SNAr electrophiles, SN2 electrophiles, Schiff base formers (SB), Acylating agents, Nonreactive and special cases (as defined by Roberts et al., 2007)
  3. The skin irritation dataset consists of 72 chemicals, labelled according to EU/GHS classification for skin irritation potential (NI - not irritating, MI - mild irritation, R38 - irritating). The data arises from several sources including the US EPA TSCA (Toxic Substances Control Act) inventory and the ECETOC databank.
    Methods

Structure representations

  1. Descriptors
  2. Fingerprints
  3. Atom environments

Similarity indices (pair wise)

  • Euclidean distance
  • Cosine similarity
  • Hodgkin-Richards Index
  • Tanimoto distance
  • Tanimoto distance on fingerprints
  • Hellinger distance on atom environments
  • Maximum Common Structure similarity

Similarity to a set

  • Similarity between a query structure and a representative point of the set (e.g. the dataset centre or a consensus fingerprint)
  • Average similarity between a query structure and the nearest k structures

Type of Descriptor:

Interfaces: Standalone application

Development status: Production

Homepage: http://ecb.jrc.it/qsar/qsar-tools/index.php?c=TOXMATCH

Dependencies:

Technical details

Data: Yes

Software: Yes

Programming language(s): Java

Operating system(s): Any

Input format: Multiple text formats

Output format: Multiple text formats

License: GPL

References

References:
Recent publication G. Patlewicz, N. Jeliazkova, A. Gallegos Saliner, A. P. Worth, Toxmatch-a new software tool to aid in the development and evaluation of chemically similar groups,SAR and QSAR in Environmental Research, 19:3, 397 — 412(2008)

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