Interpretation of nonlinear qsar models applied to ames mutagenicity data

Journal of Chemical Information and Modeling

Volumn 49, Issue 11, 2009, Pages 2551-2558

  Carlsson, Lars ^a   Helgee, Ernst Ahlberg ^a   Boyer, Scott ^a  

^a ASTRAZENECA R AND D   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL CHEMISTRY; DECISION TREES; MOLECULAR GRAPHICS; SUPPORT VECTOR MACHINES;

DATA SET; DECISION FUNCTIONS; LINEAR METHODS; LOCAL INTERPRETATION; MACHINE LEARNING METHODS; MUTAGENICITY; QSAR MODEL;

LEARNING SYSTEMS;

ALGORITHM; ARTICLE; MUTAGEN TESTING; QUANTITATIVE STRUCTURE ACTIVITY RELATION; THEORETICAL MODEL;

ALGORITHMS; MODELS, THEORETICAL; MUTAGENICITY TESTS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 72949101619     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci9002206     Document Type: Article

References (23)

1. Fox, T.; Kriegl, J. M. Curr. Top. Med. Chem 2006, 6, 1579-1591.
2. Helma, C.; Kazius, J. Curr. Comput.-Aided Drug Des. 2006, 2, 123-133.
3. Liaw, A.; Wiener, M. Breiman and Cutler's random forests for classification and regression, version 4.5-18; 2006, The Comprehensive R Archive Network. http://cran.r-project.org/doc/packages/random-Forest.pdf (accessed Jan 3, 2007).
4. Franke, L.; Byvatov, E.; Werz, O.; Steinhilber, D.; Schneider, P.; Schneider, G. J. Med. Chem. 2005, 48, 6997-7004.
5. Guha, R.; Dutta, D.; Jurs, P. C.; Chen, T. J. Chem. Inf. Model. 2006, 46, 1836-1847.
6. Wold, S.; Ruhe, A.; Wold, H.; Dunn III, W. J. SIAM J. Sci. Stat. Comput. 1984, 5, 735-743.
7. Breimann, L. Machine Learning 2001, 45, 5-32.
8. Christianini, N.; Shawe-Taylor, J. An Introduction to Support vector Machines and other kernel-based learning methods, 1st ed.; Cambridge University Press: Cambridge, United Kingdom, 2004.
9. Chang, C.-C.; Lin, C.-J. LIBSVM: a library for support vector machines; 2001; Software available at http://www.csie.ntu.edu.tw/cjlin/libsvm.
10. Wehrens, R.; Mevik, B.-H. Partial Least Squares Regression (PLSR) and Principal Component Regression (PCR), version 2.1.0; 2007, The Comprehensive R Archive Network. http://cran.r-project.org/doc/packages/pls.pdf (accessed Sep 11, 2007).
11. Daylight Theory: SMARTS - A Language for Describing Molecular Patterns. http://www.daylight.com/dayhtml/doc/theory/theory.smarts. html (accessed Jan 13, 2008)
12. Kazius, J.; McGuire, R.; Bursi, R. J. Med. Chem. 2005, 48, 312-320.
13. Faulon, J.-L.; Visco, D. P. J.; Pophale, R. S. J. Chem. Inf. Comput. Sci. 2003, 43, 707-720.
14. Faulon, J.-L.; Churchwell, C. J. J. Chem. Inf. Comput. Sci. 2003, 43, 721-734.
15. Faulon, J.-L. http://www.cs.sandia.gov/ jfaulon/QSAR/translator.tar.gz.
16. R, version 2.5.0; 2007, The R Project for Statistical Computing. http://www.r-project.org (accessed Jan 3, 2007).
17. Henshaw, W. D. J. Comput. Phys. 1994, 113, 13-25.
18. Dimitriadou, E.; Hornik, K.; Leisch, F.; Meyer, D.; Weingessel, A. Misc Functions of the Department of Statistics (e1071), TU Wien, version 1.5-16; 2006, The Comprehensive R Archive Network. http://cran.r-project.org/doc/ packages/e1071.pdf (accessed Jan 3, 2007).
19. TOXNET - Chemical Carcinogenesis Research Information System, http://toxnet.nlm.nih.gov (accessed Nov 22, 2006).
20. Young, S.; Gombar, V.; Emptage, M.; Cariello, N.; Lambert, C. Chemom. Intell. Lab. Syst. 2002, 60, 5-11.
21. Kenny, P.; Sadowski, J. Chemoinformatics Drug Discovery 2005, 271-285.
22. Openeye Scientific Software. http://www.eyesopen.com (accessed Aug 30, 2005).
23. MultiCASE Inc. http://www.multicase.com/products/prod0910.htm (accessed Jan 13, 2008)