Using graph indices for the analysis and comparison of chemical datasets

Molecular Informatics

Volumn 32, Issue 9-10, 2013, Pages 827-842

  Fourches, Denis ^a   Tropsha, Alexander ^a  

^a University of North Carolina at Chapel Hill   (United States)

Author keywords

ADDAGRA; Chemical dataset graph; Graph indices; QSAR

Indexed keywords

COMPUTATIONAL CHEMISTRY;

ADDAGRA; CHEMICAL DATASET GRAPH; CHEMICAL DESCRIPTORS; CHEMINFORMATICS; GRAPH INDEX; HIGH-DIMENSIONAL; HIGHER-DIMENSIONAL; MULTIDIMENSIONAL SPACES; QSAR; QSAR MODELING;

STATISTICAL TESTS;

ADVANCED DATASET GRAPH ANALYSIS; ANALYSIS; ARTICLE; CHEMICAL STRUCTURE; CLUSTER ANALYSIS; DATA PROCESSING; GENOMICS; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

EID: 84893421708     PISSN: 18681743     EISSN: 18681751     Source Type: Journal    
DOI: 10.1002/minf.201300076     Document Type: Article

References (33)

1. T. I. Oprea, J. Gottfries, J. Comb. Chem. 2001, 3, 157-66.
2. H. Zhu, A. Tropsha, D. Fourches, A. Varnek, E. Papa, P. Gramatica, T. Oberg, P. Dao, A. Cherkasov, I. V Tetko, J. Chem. Inf. Model. 2008, 48, 766-84.
3. P. Willett, J. M. Barnard, G. M. Downs, J. Chem. Inf. Comp. Sci. 1998, 38, 983-996.
4. P. Willett, Meth. Mol. Biol. (Clifton, NJ) 2010, 672, 133-158.
5. G. M. Downs, J. M. Barnard, Rev. Comput. Chem. 2002, 18, 1-40.
6. G. V. Paolini, R. H. B. Shapland, W. P. Van Hoorn, J. S. Mason, A. L. Hopkins, Nat. Biotechnol. 2006, 24, 805-815.
7. H. Bunke, A. Kandel, M. Last, S. Elnekave, O. Maimon, Applied Pattern Recognition, Vieweg, Braunschweig, 2003.
8. H. Bunke, K. Riesen, Pattern Recogn. 2011, 44, 1057-1067.
9. R. Khashan, W. Zheng, A. Tropsha, Proteins 2012, 80, 2207-17.
10. R. Todeschini, V. Consonni, Handbook of Molecular Descriptors, Wiley-VCH, Weinheim, Germany 2000.
11. P. Iyer, D. Dimova, M. Vogt, J. Bajorath, J. Chem. Inf. Model. 2012, 52, 1962-1969.
12. D. Gupta-Ostermann, M. Wawer, A. M. Wassermann, J. Bajorath, J. Chem. Inf. Model. 2012, 52, 935-942.
13. A. M. Wassermann, M. Wawer, J. Bajorath, J. Med. Chem. 2010, 53, 8209-8223.
14. J. Hert, M. J. Keiser, J. J. Irwin, T. I. Oprea, B. K. Shoichet, J. Chem. Inf. Model. 2008, 48, 755-65.
15. D. J. Cook, L. B. Holder, Mining Graph Data, Wiley-Interscience, New York, 2007.
16. J. Gasteiger, Anal. Bioanal. Chem. 2006, 384, 57-64.
17. M. Randic, Molecules 1998, 45, 239-252.
18. M. Randic, M. Razinger, J. Chem. Inf. Comp. Sci. 1996, 36, 429-441.
19. I. Gutman, M. Randić, Chem. Phys. Lett. 1977, 47, 15-19.
20. A. Mauri, V. Consonni, M. Pavan, R. Todeschini, Match Commun. Math. Comput. Chem. 2006, 56, 237-248.
21. A. Varnek, D. Fourches, F. Hoonakker, V. P. Solov'ev, J. Comput. Aided Mol. Des. 2005, 19, 693-703.
22. V. Austel, A. Balaban, D. Bonchev, M. Charton, T. Fujita, H. Iwamura, O. Mekenyan, I. Motoc, A. Balaban, I. Motoc, et al., Steric Effects in Drug Design, Springer, Heidelberg, 1983, pp. 21-55.
23. W. Dubitzky, M. Granzow, S. Downes, D. P. Berrar, A Practical Approach to Microarray Data Analysis (Eds: D. P. Berrar, W. Dubitzky, M. Granzow), Springer, Heidelberg, 2003, pp. 1-18.
24. D. Fourches, E. Muratov, A. Tropsha, J. Chem. Inf. Model. 2010, 50, 1189-204.
25. A. Tropsha, Mol. Inf. 2010, 29, 476-488.
26. I. V. Tetko, I. Sushko, A. K. Pandey, H. Zhu, A. Tropsha, E. Papa, T. Oberg, R. Todeschini, D. Fourches, A. Varnek, J. Chem. Inf. Model. 2008, 48, 1733-1746.
27. I. Sushko, S. Novotarskyi, R. Kçrner, A. K. Pandey, A. Cherkasov, J. Li, P. Gramatica, K. Hansen, T. Schroeter, K.-R. M-ller, et al., J. Chem. Inf. Model. 2010, 50, 2094-111.
28. T. W. Schultz, M. Hewitt, T. I. Netzeva, M. T. D. Cronin, Qsar Comb. Sci. 2007, 26, 238-254.
29. A. Varnek, D. Fourches, D. Horvath, O. Klimchuk, C. Gaudin, P. Vayer, V. Solov'ev, F. Hoonakker, I. V. Tetko, G. Marcou, Curr. Comput. Aided Drug Des. 2008, 4, 191-198.
30. J.-H. Hsieh, X. S. Wang, D. Teotico, A. Golbraikh, A. Tropsha, J. Comput. Aided Mol. Des. 2008, 22, 593-609.
31. D. Bandyopadhyay, J. Huan, J. Prins, J. Snoeyink, W. Wang, A. Tropsha, J. Comput. Aided Mol. Des. 2009, 23, 773-84.
32. D. Fourches, D. Pu, A. Tropsha, Comb. Chem. High Throughput. Scr. 2011, 14, 217-225.
33. D. Fourches, D. Pu, C. Tassa, R. Weissleder, S. Y. Shaw, R. J. Mumper, A. Tropsha, ACS Nano 2010, 4, 5703-5712.