Compressed binary bit trees: A new data structure for accelerating database searching

Journal of Chemical Information and Modeling

Volumn 49, Issue 2, 2009, Pages 257-262

  Smellie, Andrew ^a  

^a CambridgeSoft Corporation   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINARY TREES; DATABASE SYSTEMS; INDEXING (OF INFORMATION); SEARCH ENGINES;

BIT-STRINGS; DATABASE SEARCHING; SEARCH PARAMETERS; SIMILARITY SEARCHING; TANIMOTO COEFFICIENT;

TREES (MATHEMATICS);

EID: 65249127524     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci800325v     Document Type: Article

References (22)

1. Willett, P.; Barnard, J. M.; Downs, G. M. Chemical Similarity Searching. J. Chem. Inf. Comput. Sci. 1998, 38 (6), 983-996.
2. Flower, D. R. On the Properties of Bit String-Based Measures of Chemical Similarity. J. Chem. Inf. Comput. Sci. 1998, 38 (3), 379-386.
3. Daylight Chemical Information Systems, 120 Vantis-Suite 550-Aliso Viejo, CA 92656. http://www.daylight.com/dayhtml/doc/theory/theory. finger.html (accessed Jan 2009).
4. Tanimoto, T. T. IBM Internal Report; Nov 17, 1957.
5. As a representative of many example papers, see: (a) Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Molecular Similarity Searching using Atom Environments, Information-Based Feature Selection and a Naïve Bayesian Classifier. J. Chem. Inf. Comput. Sci. 2004, 44, 170-178.
6. Dunkel, M.; Günther, S.; Ahmed, J.; Wittig, B.; Preissner, R. SuperPred: drug classification and target prediction. Nucleic Acids Res. 2008, Jul 1; 36(Web Server issue):W55-9. .
7. Daylight Chemical Information Systems, 120 Vantis-Suite 550-Aliso Viejo, CA 92656. http://www.daylight.com/dayhtml/doc/theory/theory. merlin.html (accessed Jan 2009).
8. Swadimass, S. J.; Baldi, P. Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time. J. Chem. Inf. Model. 2007, 47, 302-317.
9. Xue, L.; Stahura, F.; Bajorath, J. Similarity Search Profiling Reveals Effects of Fingerprint Scaling in Virtual Screening. J. Chem. Inf. Model. 2004, 44, 2032-2039.
10. Solomon, B. ChemBioNews; 2006; 16.2. http://chembionews. cambridgesoft.com/Articles/Default.aspx?articleID=378 (accessed Jan 2009).
11. http://www.merckbooks.com/mindex/index.html (accessed Jan 2009).
12. Schreiman, I. ChemBioNews; 2005; 15.3. http://www.cambridgesoft. com/webinars/info/?webinarid=80 (accessed Jan 2009).
13. Schreiman, I. ChemBioNews; 2005;. 13.3. http://chembionews. cambridgesoft.com/Articles/Default.aspx?articleID=343 (accessed Jan 2009).
14. The NCI Database distributed by CambridgeSoft Inc. http://nci. cambridgesoft.com/ (accessed Jan 2009).
15. The TCM Database distributed by CambridgeSoft Inc. http://www. cambridgesoft.com/databases/details/?db=3 (accessed Jan 2009).
16. The Nanogen Database distributed by CambridgeSoft Inc. http:// www.cambridgesoft.com/databases/details/?db=22 (accessed Jan 2009).
17. The Ashgate Database distributed by CambridgeSoft Inc. http:// www.cambridgesoft.com/databases/details/?db=2 (accessed Jan 2009).
18. http://www.daylight.com/dayhtml/doc/theory/theory.finger.html (accessed Jan 2009).
19. Furst, A. Oracle Cartridge 11.0 internal documentation; Cambridge-Soft Inc.
20. Bender, A.; Glen, R. C. Molecular similarity: a key technique in molecular informatics. Org. Biomol. Chem. 2004, 2, 3204-3218.
21. Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Similarity searching of chemical databases using atom environment descriptors: evaluation of performance (MOLPRINT 2D). J. Chem. Inf. Comput. Sci. 2004, 44, 1708-1718.
22. Held, G. Data Compression: Techniques and Applications, Hardware and Software Considerations; 2nd ed.; John Wiley & Sons: New York, NY, 1987.