Computational derivation of structural alerts from large toxicology data sets

Journal of Chemical Information and Modeling

Volumn 54, Issue 10, 2014, Pages 2945-2952

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

^a ASTRAZENECA R AND D   (Sweden)

^b Swedish Toxicology Sciences Research Center (Swetox)   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ENGINEERING; CHEMISTRY;

ACCURATE PREDICTION; AUTOMATIC METHOD; AUTOMATIC RETRIEVAL; END POINTS; IDENTIFICATION METHOD; MANUAL ANALYSIS; MUTAGENICITY; VALIDATION STUDY;

CHEMICAL ANALYSIS;

MOLECULAR LIBRARY; MUTAGENIC AGENT;

ANIMAL; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; DRUG DESIGN; HUMAN; INFORMATION PROCESSING; MOLECULAR LIBRARY; MUTAGEN TESTING; PREDICTIVE VALUE; STRUCTURE ACTIVITY RELATION; TOXICITY;

ANIMALS; COMPUTER SIMULATION; DATASETS AS TOPIC; DRUG DESIGN; HUMANS; MODELS, CHEMICAL; MOLECULAR CONFORMATION; MUTAGENICITY TESTS; MUTAGENS; PREDICTIVE VALUE OF TESTS; SMALL MOLECULE LIBRARIES; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84908233587     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci500314a     Document Type: Article

References (26)

1. Ashby, J.; Tennant, R. W. Chemical structure, Salmonella mutagenicity and extent of carcinogenicity as indicators of genotoxic carcinogenesis among 222 chemicals tested in rodents by the U.S. NCI/NTP Mutat. Res. Rev. Genet. 1988, 204, 17-115
2. Ashby, J.; Tennant, R. W. Definitive relationships among chemical structure, carcinogenicity and mutagenicity for 301 chemicals tested by the U.S. NTP Mutat. Res. Rev. Genet. 1991, 257, 229-306
3. Johnson, D. E.; Blower, P. E.; Myatt, G. J.; Wolfgang, G. H. I. Chem-tox informatics: data mining using a medicinal chemistry building block approach Curr. Opin. Drug Discovery Dev. 2001, 18, 76-79
4. Leadscope-Chemoinformatics Platform for Drug Discovery; http://www.leadscope.com/index.php (accessed Feb 7, 2014).
5. Klopman, G. MULTICASE. 1. A Hierarchical Computer Automated Structure Evaluation Program Quantum Struct.-Act. Relat. 1992, 11, 176-184
6. MultiCASE Inc; http://www.multicase.com/products/prod01.htm (accessed Oct 9, 2010.
7. Sanderson, D.; Earnshaw, C. Computer Prediction of Possible Toxic Action from Chemical Structure; The DEREK System Hum. Exp. Toxicol. 1991, 10, 261-273
8. DEREK; Lhasa LTD, 2009; http://www.lhasalimited.org/products/derek-nexus.htm.
9. Deshpande, M.; Kuramochi, M.; Wale, N.; Karypis, G. Frequent Substructure-Based Approaches for Classifying Chemical Compounds IEEE Trans. Knowl. Data Eng. 2005, 17, 1036-1050
10. Nicolaou, C. A.; Tamura, S. Y.; Kelly, B. P.; Bassett, S. I.; Nutt, R. F. Analysis of Large Screening Data Sets via Adaptively Grown Phylogenetic-Like Trees J. Chem. Inf. Comput. Sci. 2002, 42, 1069-1079
11. Faulon, J.-L.; Visco, D. P. J.; Pophale, R. S. Signature Molecular Descriptor. 1. Using Extended Valence Sequences in QSAR and QSPR Studies J. Chem. Inf. Comput. Sci. 2003, 43, 707-720
12. Faulon, J.-L.; Churchwell, C. J. Signature Molecular Descriptor. 2. Enumerating Molecules from Their Extended Valence Sequences J. Chem. Inf. Comput. Sci. 2003, 43, 721-734
13. Kazius, J.; McGuire, R.; Bursi, R. Derivation and Validation of Toxicophores for Mutagenicity Prediction J. Med. Chem. 2005, 48, 312-320
14. Young, S.; Gombar, V.; Emptage, M.; Cariello, N.; Lambert, C. Mixture Deconvolution and Analysis of Ames Mutagenicity Data Chemom. Intell. Lab. Syst. 2002, 60, 5-11
15. Steinbeck, C.; Han, Y.; Kuhn, S.; Horlacher, O.; Luttmann, E.; Willighagen, E. The Chemistry Development Kit (CDK) An Open-Source Java Library for Chemo- and Bioinformatics J. Chem. Inf. Comput. Sci. 2003, 43, 493-500 12653513
16. Benjamini, Y.; Hochberg, Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing J. R. Stat. Soc., Ser. B: Stat. Methodol. 1995, 57, 289-300
17. Ogham 2D Chemical Structure Layout and Rendering; http://www.eyesopen.com/docs/ogham/1.7.0/html/index.html (accessed on Jan 3, 2011).
18. Dalby, A.; Nourse, J. G.; Hounshell, W. D.; Gushurst, A. K. I.; Grier, D. L.; Leland, B. A.; Laufer, J. Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited J. Chem. Inf. Comput. Sci. 1992, 32, 244-255
19. The Open Babel Package; http://openbabel.org/wiki/Main-Page (accessed on Mar 2, 2014).
20. SMARTS; http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html (accessed Aug 7, 2010).
21. Openeye Scientific Software; http://www.eyesopen.com (accessed Aug 7, 2010).
22. Kuramochi, M.; Karypis, G. An Efficient Algorithm for Discovering Frequent Subgraphs IEEE Trans. Knowl. Data Eng. 2004, 16, 1038-1051
23. Faulon, J.-L. Isomorphism, Automorphism Partitioning, and Canonical Labeling Can Be Solved in Polynomial-Time for Molecular Graphs J. Chem. Inf. Comput. Sci. 1998, 38, 432-444
24. Klopman, G. Artificial intelligence approach to structure-activity studies. Computer automated structure evaluation of biological activity of organic molecules J. Am. Chem. Soc. 1984, 106, 7315-7321
25. Klopman, G.; McGonigal, M. Computer simulation of physical-chemical properties of organic molecules. 1. Molecular system identification J. Chem. Inf. Comput. Sci. 1981, 21, 48-52
26. Ahlberg Helgee, E.; Carlsson, L.; Boyer, S. A Method for Automated Molecular Optimization Applied to Ames Mutagenicity Data J. Chem. Inf. Model. 2009, 49, 2559-2563 19877655