Scalable partitioning and exploration of chemical spaces using geometric hashing

Journal of Chemical Information and Modeling

Volumn 46, Issue 1, 2006, Pages 321-333

  Dutta, Debojyoti ^a   Guha, Rajarshi ^b   Jurs, Peter C ^b   Chen, Ting ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; DATA MINING; DESCRIBING FUNCTIONS; HEURISTIC METHODS; REGRESSION ANALYSIS; SCREENING; VIRTUAL REALITY;

INFORMATICS; LOCALITY-SENSITIVE HASHING (LSH); VIRTUAL SCREENING (VS);

DRUG PRODUCTS;

EID: 33244462202     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci050403o     Document Type: Conference Paper

References (35)

1. Jorgensen, W. Design and Diversity Analysis of Large Combinatorial Libraries Using Cell-Based Methods. Science 2004, 303, 1813-1818.
2. Datar, M.; Immorlica, N.; Indyk, P.; Mirrokni, V. S. Locality-sensitive hashing scheme based on p-stable distributions. In SCG '04: Proceedings of the twentieth annual symposium on Computational geometry; ACM Press: New York, 2004.
3. Stahura, F.; Bajorath, J. Virtual screening methods that complement HTS. Comb. Chem. High Throughput Screening 2004, 7, 259-269.
4. Xu, H.; Agrafiotis, D. Nearest Neighbor Search in General Metric Spaces Using a Tree Data Structure with a Simple Heuristic. J. Chem. Inf. Comput. Sci. 2003, 43, 1933-1941.
5. Cover, T.; Hart, P. Nearest Neighbor Pattern Classification. IEEE Trans. Inf. Theory 1967, 13, 21-7.
6. Pearlman, R.; Smith, K. Metric Validation And The Receptor-Relevant Subspace Concept. J. Chem. Inf. Comput. Sci. 1999, 39, 28-35.
7. Pearlman, R.; Smith, K. Novel Software Tools For Chemical Diversity. Perspect. Drug Discovery Des. 1998, 339-353.
8. Schnur, D. Design and Diversity Analysis of Large Combinatorial Libraries Using Cell-Based Methods. J. Chem. Inf. Comput. Sci. 1999, 39, 36-45.
9. Gasteiger, J. Chemoinformatics, A Textbook; John Wiley & Sons: Weinheim, Germany, 2003.
10. Duda, R.; Hart, P. Pattern Classification, 2nd ed.; Wiley-Interscience: Hoboken, NJ; 1998.
11. Hastic, T.; Tibshirani, R.; Friedman, J. An Introduction to Statistical Machine Learning; Spinger Verlag: New York, 2001.
12. Guha, S.; Meyerson, A.; Mishra, N.; Motwani, R.; O'Callaghan, L. Clustering Data Streams: Theory and Practice. IEEE Trans. Knowledge Data Eng. 2003, 15, 515-528.
13. Gionis, A.; Indyk, P.; Motwani, R. Similarity Search in High Dimensions via Hashing. In VLDB '99: Proceedings of the 25th International Conference on Very Large Data Bases; Morgan Kaufmann Publishers Inc.: San Francisco, CA, 1999.
14. Agrafiotis, D. A Constant Time Algorithm for Estimating the Diversity of Large Chemical Libraries. J. Chem. Inf. Comput. Sci. 2001, 41, 159-167.
15. Garey, R.; Johnson, D. Computers and Intractibility; W. H. Freeman: New York, 1979.
16. Kazius, J.; McGuire, R.; Bursi, R. Derivation and Validation of Toxicophores for Mutagenicity Prediction. J. Med. Chem. 2005, 48, 312-320.
17. Ames, B. N.; McCann, H.; Yamasaki, E. Methods for detecting carcinogens and mutagens with the Salmonella/mammalian-microsome mutagenicity test. Mutat. Res. 1975, 31, 347-364.
18. http://cactus.nci.nih.gov/DownLoad/AID2DA99.sdz.
19. Voigt, J.; Bienfait, B.; Wang, S.; Nicklaus, M. Comparison of the Open NCI Database with Seven Large Chemical Structural Databases. J. Chem. Inf. Comput. Sci. 2001, 41, 702-712.
20. Molecular Operating Environment (MOE 2004.03); Chemical Computing Group Inc.: Montreal, Quebec, Canada.
21. http://cactus.nci.nih.gov/DownLoad/NCI3DA99.sdz.
22. MACCS Fingerprints; MDL Information Systems Inc.: SanLeandro, CA.
23. Wiener, H. Structural Determination of Paraffin Boiling Points. J. Am. Chem. Soc. 1947, 69, 17-20.
24. Balaban, A. Higly discriminating distance based topological index. Chem. Phys. Lett. 1982, 89, 399-404.
25. Kier, L.; Hall, L. Molecular Connectivity in Chemistry and Drug Research; Academic Press: New York, 1976.
26. Kier, L. A shape index from molecular graphs. Quant. Struct.-Act. Relat. Pharmacol., Chem. Biol. 1985, 4, 109-116.
27. Kier, L. Shape indexes for orders one and three from molecular graphs. Quant. Struct.-Act. Relat. Pharmacol., Chem. Biol. 1986, 5, 1-7.
28. Kier, L. Distinguishing atom differences in a molecular graph index. Quant. Struct.-Act. Relat. Pharmacol., Chem. Biol. 1986, 5, 7-12.
29. Kier, L.; Hall, L.; Murray, W. Molecular Connectivity I: Relationship to local anasthesia. J. Pharm. Sci. 1975, 64, 1971-1974.
30. Kier, L.; Hall, L. Molecular Connectivity in Structure Activity Analysis; John Wiley & Sons: Hertfordshire, England, 1986.
31. Kier, L.; Hall, L. Molecular Connectivity VII: Specific treatment to heteroatoms. J. Pharm. Sci. 1976, 65, 1806-1809.
32. Gasteiger, J.; Marsili, M. A New Model for Calculating Atomic Charges in Molecules. Tetrahedron Lett. 1978, 34, 3181-3184.
33. Gasteiger, J.; Marsili, M. Iterative partial equalization of orbital elektronegativity - a rapid access to atomic charges. Tetrahedron 1980, 36, 3219-3228.
34. Ertl, P.; Rohde, B.; Selzer, P. Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment Based Contributions and Its Application to the Prediction of Drug Transport Properties. J. Med. Chem. 2000, 43, 3714-3717.
35. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2004; ISBN 3-900051-07-0.