Publicly-accessible QSAR software tools developed by the Joint Research Centre

To promote the availability of reliable computer-based estimation methods for use in the regulatory assessment of chemicals, the European Chemicals Bureau (ECB) within the European Commission's Joint Research Centre (JRC) has developed a range of user-friendly and freely available software tools. The article gives an overview of four of these tools, explaining their main functionalities and applicability: Toxtree, Toxmatch, DART and the JRC QSAR Model Database. Toxtree predicts different types of toxicological hazard and modes of action by applying decision tree approaches; it can be used for initial hazard assessments. Toxmatch is a tool for chemical similarity assessment; it can be used to compare model training and test sets, to facilitate the formation of chemical categories and to support the application of read-across between analogues. DART (Decision Analysis by Ranking Techniques) provides a variety of Multi-criteria Decision Making (ranking) methods, and can be used to support the ranking of chemicals according to their environmental and toxicological concern. Finally, the JRC QSAR Model Database is a web-based inventory of (Q)SAR models to help industry and government authorities to identify suitable (Q)SARs for chemicals undergoing regulatory review. †Presented at the 13th International Workshop on QSARs in the Environmental Sciences (QSAR 2008), 8–12 June 2008, Syracuse, USA.

[1]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[2]  Michael M. Cone,et al.  Molecular structure comparison program for the identification of maximal common substructures , 1977 .

[3]  F. McLafferty,et al.  Computer-aided interpretation of mass spectra. 20. Molecular structure comparison program for the identification of maximal common substructures , 1977 .

[4]  R A Ford,et al.  Estimation of toxic hazard--a decision tree approach. , 1978, Food and cosmetics toxicology.

[5]  Denis Bouyssou,et al.  Building Criteria: A Prerequisite for MCDA , 1990 .

[6]  J. Hermens,et al.  Classifying environmental pollutants , 1992 .

[7]  B. Hobbs,et al.  Multicriteria methods for resource planning: an experimental comparison , 1994 .

[8]  C. Russom,et al.  Predicting modes of toxic action from chemical structure: Acute toxicity in the fathead minnow (Pimephales promelas) , 1997 .

[9]  Benjamin F. Hobbs,et al.  Building public confidence in energy planning : a multimethod MCDM approach to demand-side planning at BC gas , 1997 .

[10]  Robert S. Boethling,et al.  Improved method for estimating bioconcentration/bioaccumulation factor from octanol/water partition coefficient , 1999 .

[11]  J. Hermens,et al.  Classifying environmental pollutants: Part 3. External validation of the classification system. , 2000, Chemosphere.

[12]  Robert C. Glen,et al.  Novel Methods for the Prediction of logP, pKa, and logD , 2002, J. Chem. Inf. Comput. Sci..

[13]  Hugo Kubinyi,et al.  Chemical similarity and biological activities , 2002 .

[14]  C. Steinbeck,et al.  The Chemistry Development Kit (CDK): An Open‐Source Java Library for Chemo‐ and Bioinformatics. , 2003 .

[15]  Sharon Munn,et al.  Assessment of additional testing needs under REACH Effects of (Q)SARS, risk based testing and voluntary industry initiatives , 2003 .

[16]  N. Nikolova,et al.  International Union of Pure and Applied Chemistry, LUMO energy ± The Lowest Unoccupied Molecular Orbital (LUMO) , 2022 .

[17]  I Kimber,et al.  Classification of contact allergens according to potency: proposals. , 2003, Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association.

[18]  Egon L. Willighagen,et al.  The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo-and Bioinformatics , 2003, J. Chem. Inf. Comput. Sci..

[19]  Andreas Bender,et al.  Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naïve Bayesian Classifier , 2004, J. Chem. Inf. Model..

[20]  Manuela Pavan,et al.  New indices for analysing partial ranking diagrams , 2004 .

[21]  John D. Walker,et al.  Use of Physicochemical Property Limits to Develop Rules for Identifying Chemical Substances with no Skin Irritation or Corrosion Potential , 2004 .

[22]  Jose Cotovio,et al.  The In Vitro Acute Skin Irritation of Chemicals: Optimisation of the EPISKIN Prediction Model within the Framework of the ECVAM Validation Process , 2005, Alternatives to laboratory animals : ATLA.

[23]  Elisabeth Schmidt,et al.  The EpiDerm Test Protocol for the Upcoming ECVAM Validation Study on In Vitro Skin Irritation Tests — An Assessment of the Performance of the Optimised Test , 2005, Alternatives to laboratory animals : ATLA.

[24]  Horst Spielmann,et al.  Assessment of the Eye Irritating Properties of Chemicals by Applying Alternatives to the Draize Rabbit Eye Test: The Use of QSARs and In Vitro Tests for the Classification of Eye Irritation , 2005, Alternatives to laboratory animals : ATLA.

[25]  John D. Walker,et al.  The Skin Irritation Corrosion Rules Estimation Tool (SICRET) , 2005 .

[26]  John D. Walker,et al.  Use of structural alerts to develop rules for identifying chemical substances with skin irritation or skin corrosion potential , 2005 .

[27]  Ian Kimber,et al.  Compilation of Historical Local Lymph Node Data for Evaluation of Skin Sensitization Alternative Methods , 2005, Dermatitis : contact, atopic, occupational, drug.

[28]  Petra S Kern,et al.  Mechanistic applicability domain classification of a local lymph node assay dataset for skin sensitization. , 2007, Chemical research in toxicology.

[29]  Worth Andrew,et al.  The Use of Computational Methods in the Grouping and Assessment of Chemicals - Preliminary Investigations , 2007 .

[30]  M. Pavan,et al.  The role of the European Chemicals Bureau in promoting the regulatory use of (Q)SAR methods , 2007, SAR and QSAR in environmental research.

[31]  Worth Andrew,et al.  A Compendium of Case Studies that Helped to Shape the REACH Guidance on Chemical Categories and Read Across , 2007 .

[32]  Valérie Zuang,et al.  The ECVAM International Validation Study on In Vitro Tests for Acute Skin Irritation: Selection of Test Chemicals , 2007, Alternatives to laboratory animals : ATLA.

[33]  J Jaworska,et al.  How can structural similarity analysis help in category formation? , 2007, SAR and QSAR in environmental research.

[34]  G. Patlewicz,et al.  An evaluation of the implementation of the Cramer classification scheme in the Toxtree software , 2008, SAR and QSAR in environmental research.

[35]  Manuela Pavan,et al.  A set of case studies to illustrate the applicability of DART (Decision Analysis by Ranking Techniques) in the ranking of chemicals , 2008 .

[36]  Romualdo Benigni,et al.  The Benigni / Bossa rulebase for mutagenicity and carcinogenicity - a module of Toxtree , 2008 .

[37]  G Patlewicz,et al.  Toxmatch–a new software tool to aid in the development and evaluation of chemically similar groups , 2008, SAR and QSAR in environmental research.

[38]  Guidance on information requirements and chemical safety assessment , 2008 .