Pharmacophore alignment search tool: Influence of canonical atom labeling on similarity searching

Journal of Computational Chemistry

Volumn 31, Issue 15, 2010, Pages 2810-2826

  Hähnke, Volker ^a,b   Rupp, Matthias ^c   Krier, Mireille ^d   Rippmann, Friedrich ^d   Schneider, Gisbert ^b  

^a GOETHE UNIVERSITY   (Germany)

^b ETH ZURICH   (Switzerland)

^c INSTITUTE OF EPIDEMIOLOGY   (Germany)

^d Merck Serono GmbH   (Germany)

Author keywords

global alignment; line notation; molecular graph; similarity; virtual screening

Indexed keywords

GLOBAL ALIGNMENT; LINE NOTATION; MOLECULAR GRAPHS; SIMILARITY; VIRTUAL SCREENING;

PHARMACODYNAMICS;

ALIGNMENT;

ALGORITHM; ARTICLE; BIOLOGY; DRUG DEVELOPMENT; FACTUAL DATABASE; METHODOLOGY; MOLECULAR LIBRARY; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ALIGNMENT;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; DRUG DISCOVERY; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ALIGNMENT; SMALL MOLECULE LIBRARIES;

EID: 78149443581     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21574     Document Type: Article

References (42)

1. Hähnke, V.,;, Hofmann, B.,;, Grgat, T.,;, Proschak, E.,;, Steinhilber, D.,;, Schneider, G., J Comput Chem 2009, 30, 761.
2. Weininger, D.,;, Weininger, A.,;, Weininger, J. L., J Chem Inf Comput Sci 1989, 29, 97.
3. Needleman, S. B.,;, Wunsch, C. D., J Mol Biol 1970, 48, 443.
4. Durbin, R.,;, Eddy, S. R.,;, Krogh, A.,;, Mitchison, G., Biological Sequence Analysis; Cambridge University Press: Cambridge, 1998.
5. Truchon, J. F.,;, Bayly, C. I., J Chem Inf Model 2007, 47, 488.
6. Pearson, K., Phil Trans R Soc 1896, 187, 253.
7. Kendall, M., Biometrika 1938, 30, 81.
8. Brenner, S. E.,;, Chothia, C.,;, Hubbard, T. J. P., Proc Natl Acad Sci USA 1998, 95, 6073.
9. Karlin, S.,;, Altschul, S. F., Proc Natl Acad Sci USA 1990, 87, 2264.
10. Jochum, C.,;, Gasteiger, J., J Chem Inf Comput Sci 1977, 17, 113.
11. Prabhakar, Y. S.,;, Balasubramanian, K., J Chem Inf Model 2006, 46, 52.
12. Pearson, K., Philos Mag 1901, 2, 559.
13. Belkin, M.,;, Niyogi, P., Neural Comput 2003, 15, 1373.
14. Tenenbaum, J. B.,;, de Silva, V.,;, Langford, J. C., Science 2000, 290, 2319.
15. Shaw, B.,;, Jebara, T., Proceedings of the Eleventh International Conference on Artificial Intelligence and Statistics; Omnipress: Madison, 2007.
16. Schneider, P.,;, Schneider, G., QSAR Comb Sci 2003, 22, 713.
17. Zhao, W.,;, Hevener, K. E.,;, White, S. W.,;, Lee, R. E.,;, Boyett, J. M., BMC Bioinformatics 2009, 10, 225.
18. Massey, F. J., J Am Stat Ass 1951, 46, 68.
19. Proschak, E.,;, Wegner, J. K.,;, Schüller, A.,;, Schneider, G.,;, Fechner, U., J Chem Inf Model 2007, 47, 295.
20. Vingron, M.,;, Waterman, M. S., J Mol Biol 1994, 235, 1.
21. Morgan, H. L., J Chem Doc 1965, 5, 107.
22. Cover, T.,;, Hart, P., IEEE Trans Info Theory 1967, 13, 21.
23. Müller-Hannemann, M.,;, Schwartz, A., J Exp Algor 2000, 5.
24. Floyd, R. W., Comm ACM 1962, 5, 345.
25. Warshall, S., J ACM 1962, 9, 11.
26. Schölkopf, B.,;, Smola, A.,;, Müller, K., Neural Comput 1998, 10, 1299.
27. Kondor, R. I.,;, Lafferty, J. D., Proceedings of the Nineteenth International Conference on Machine Learning; Morgan Kaufmann Publishers Inc.: San Francisco, 2002.
28. Tsuda, K.,;, Noble, W. S., Bioinformatics 2004, 20, 326.
29. Doolin, D.,;, Dongarra, J.,;, Seymour, K., Sci Program 1999, 7, 111.
30. Borchers, B., Opt Meth Soft 1999, 11, 613.
31. Rupp, M., Kernel Methods for Virtual Screening; Johann Wolfgang Goethe-University: Frankfurt am Main, 2009.
32. Faulon, J. L.,;, Collins, M. J.,;, Carr, R. D., J Chem Inf Comput Sci 2004, 44, 427.
33. Smola, A. J.,;, Kondor, R. I., Proceedings of the 16th Annual Conference on Computational Learning Theory and 7th Kernel Workshop; Springer: Berlin and Heidelberg, 2003.
34. Shaw, B.,;, Jebara, T., Proceedings of the 26th International Conference on Machine Learning; Omnipress: Madison, 2009.
35. Damerau, F. J., Commun ACM 1964, 7, 171.
36. Newberg, L. A., J Comput Biol 2008, 15, 1187.
37. Chia, N.,;, Bundschuh, R., J Comput Biol 2006, 13, 429.
38. Hartmann, A. K., Phys Rev E 2002, 65, 056102.
39. Lipman, D. J.,;, Pearson, W. R., Science 1985, 227, 1435.
40. Booth, H. S.,;, Maindonald, J. H.,;, Wilson, S. R.,;, Gready, J. E., J Comput Biol 2004, 11, 616.
41. Krier, M.,;, Hutter, M. C., J Chem Inf Model 2009, 49, 1280.
42. Dayhoff, M. O.,;, Schwartz, R. M.,;, Orcutt, B. C., Atlas of Protein Sequence and Structure; National Biomedical Research Foundation: Washington, DC, 1978.