AMBIT-SMARTS: Efficient searching of chemical structures and fragments

Molecular Informatics

Volumn 30, Issue 8, 2011, Pages 707-720

  Jeliazkova, Nina ^a   Kochev, Nikolay ^b  

^a IDEACONSULT LTD   (Bulgaria)

^b UNIVERSITY OF PLOVDIV   (Bulgaria)

Author keywords

Benchmark; Database; Screening; SMARTS; Subgraph isomorphism; Substructure searching

Indexed keywords

COMPUTATIONAL LINGUISTICS; OPEN SOURCE SOFTWARE; OPEN SYSTEMS; QUERY LANGUAGES; SET THEORY; SOFTWARE PACKAGES; SYNTACTICS; WEBSITES;

BENCHMARK; LANGUAGE SPECIFICATION; OPEN-SOURCE SOFTWARES; PERFORMANCE; SMARTS; STRUCTURAL FRAGMENTS; SUBGRAPH ISOMORPHISM; SUBSTRUCTURE SEARCHING; SYNTAX EXTENSION; WEBS SERVICES;

WEB SERVICES;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMOINFORMATICS; COMPUTER PROGRAM; DATA BASE; INFORMATION SCIENCE; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; SCREENING;

EID: 80052090509     PISSN: 18681743     EISSN: 18681751     Source Type: Journal    
DOI: 10.1002/minf.201100028     Document Type: Article

References (30)

1. J. Gasteiger, T. Engel, in Chemoinformatics: a Textbook, Wiley-VCH, 2003, ch. 1.
2. J. Gasteiger, T. Engel, in Chemoinformatics: a Textbook, Wiley-VCH, 2003, ch. 6.
3. N. Jeliazkova, J. Jaworska, A. P. Worth, in In Silico Toxicology: Principles and Applications (Issues in Toxicology (Ed:, Marc Cronin,)), Royal Society of Chemistry, London. 2010, pp. 408-443.
4. http://ambit.sourceforge.net/, accessed 25 Feb 2010.
5. D. Weininger, J. Chem. Inf. Comput. Sci. 1988, 28, 31-36.
6. C. Steinbeck, Y. Han, S. Kuhn, O. Horlacher, E. Luttmann, E. L. Willighagen, J. Chem. Inf. Comput. Sci. 2003, 43(2), 493-500.
7. C. Steinbeck, C. Hoppe, S. Kuhn, M. Floris, R. Guha, E. L. Willighagen, Curr. Pharm. 2006, 17, 2111-2120.
8. OpenEye, http://www.eyesopen.com/, accessed Feb 25, 2011.
9. Molecular Operating Environment (MOE), http://www.chemcomp.com/software. htm, accessed Feb 25, 2011.
10. OpenBabel, http://openbabel.org, accessed Feb 25, 2011.
11. MySQL, http://mysql.com/, accessed Feb 25, 2011.
12. S. Ash, M. A. Cline, R.W Homer, T. Hurst, G. B. Smith, J. Chem. Inf. Comput. Sci. 1997, 37, 71-79.
13. http://www.iupac.org/inchi/, accessed Feb 25, 2011.
14. http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html, accessed 25 Feb 2011.
15. V. Prelog, G. Helmchen, Angew. Chem. Int. Ed. Engl. 1982, 21, 567-654.
16. M. Garey, D. Johnson, Computers and Intractability; A Guide to the Theory of NP-Completeness, W.H. Freeman, New York, 1979.
17. L. C. Ray, R. A. Kirsch, Science 1957, 126, 814-819.
18. S. Asad Rahman, M. Bashton, G.L. Holliday, R. Schrader, J.M. Thornton: J. Cheminform. 2009, 1 : 12 doi:10.1186/1758-2946-1-12.
19. JoeLib, http://www.ra.cs.uni-tuebingen.de/software/joelib/ accessed 25 Feb 2011.
20. EINECS, http://ecb.jrc.ec.europa.eu/qsar/information-sources/ec- inventory/, accessed 25 Feb 2011.
21. http://apps.echa.europa.eu/preregistered/preregistered-sub.aspx, accessed 25 Feb 2011.
22. http://toxtree.sourceforge.net, accessed 25 Feb 2011.
23. http://tomcat.apache.org/, accessed Feb 25, 2011.
24. http://opentox.org, accessed Feb 25, 2011.
25. B. Hardy, N. Douglas, C. Helma, M. Rautenberg, N. Jeliazkova, V. Jeliazkov, I. Nikolova, R. Benigni, O. Tcheremenskaia, S. Kramer, T. Girschick, F. Buchwald, J. Wicker, A. Karwath, M. Gütlein, A. Maunz, H. Sarimveis, G. Melagraki, A. Afantitis, P. Sopasakis, D. Gallagher, V. Poroikov, D. Filimonov, A. Zakharov, A. Lagunin, T. Gloriozova, S. Novikov, N. Skvortsova, D. Druzhilovsky, S. Chawla, I. Ghosh, S. Ray, H. Patel, S. Escher, J. Cheminform. 2010, 2: 7.
26. http://toxpredict.org, accessed Feb 25, 2011.
27. A. C. Lee, J. Yu, G. M. Crippen, J. Chem. Inf. Model 2008, 48 (10), 2042-2053.
28. G. Patlewicz, N. Jeliazkova, R. J. Safford, A. P. Worth, B. Aleksiev, SAR QSAR Environ Res. 2008, 19(5-6), 495-524.
29. B. Bhhatarai, W. Teetz, T. Liu, T. Öberg, N. Jeliazkova, N. Kochev, O. Pukalov, I. Tetko, S. Kovarich, E. Papa, P. Gramatica, Mol. Inf. 2010, 28, 189.
30. http://www.cadaster.eu/, accessed Feb 25, 2011.