An efficient implementation of distance-based diversity measures based on k-d trees

Journal of Chemical Information and Computer Sciences

Volumn 39, Issue 1, 1999, Pages 51-58

  Agrafiotis, Dimitris K ^a   Lobanov, Victor S ^a  

^a JOHNSON AND JOHNSON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0001916126     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci980100c     Document Type: Article

References (25)

1. Martin, E. J.; Blariey, J. M.; Siani, M. A.; Spellmeyer, D. C.; Wong, A. K.; Moos, W. H. J. Med. Chem. 1995, 38, 1431-1436.
2. Agrafiotis, D. K. Molecular Diversity. In Encyclopedia of Computational Chemistry; Wiley: New York, in press.
3. Agrafiotis, D. K.; Myslik, J. M.; Salemme, F. R. Advances in diversity profiling and combinatorial series design. In Annual Reviews in Combinatorial Chemistry and Molecular Diversity; in press.
4. Martin, E. J.; Spellmeyer, D. C.; Critchlow, R. E., Jr.; Blaney, J. M. Does combinatorial chemistry obviate computer-aided drug design? In Reviews in Computational Chemistry; Lipkowitz, K. B.; Boyd, D. B., Eds.; VCH: New York, 1997; Vol. 10, Chapter 2, p 75.
5. Turner, D. B.; Tyrrell, S. M.; Willett, P. Rapid quantification of molecular diversity for selective database aqcuisition. J. Chem. Inf. Comput. Sci. 1997, 37, 18-22.
6. Lajiness, M. S. In QSAR: Rational Aproaches to the Design of Bioactive Compounds; Silipo, C., Vittoria, A., Eds.; Elsevier: Amsterdam, 1991; pp 201-204.
7. Polinsky, A.; Feinstein, R. D.; Shi, S.; Kuki, A. In Molecular Diversity and Combinatorial Chemistry; Chaiken, I. M.; Janda, K. D., Eds.; American Chemical Society: Washington DC, 1996; pp 219-232.
8. Agrafiotis, D. K. Stochastic algorithms for maximizing molecular diversity. 3-rd Electronic Computational Chemistry Conference, http://hackberry.chem.niu.edu/ECCC3/paper48, 1996.
9. Agrafiotis, D. K. Stochastic algorithms for maximizing molecular diversity. J. Chem. Inf. Comput. Sci. 1997, 37(5), 841-851.
10. Hassan, M.; Bielawski, J. P.; Hempel, J. C.; Waldman, M. Mol. Divers. 1996, 2, 64-74.
11. Bentley, J. L. Multidimensional binary search trees used for associative searching. Comm. ACM 1975, 18(9), 509-517.
12. Friedman, J. H.; Bentley, J. L.; Finkel, R. A. An algorithm for finding best matches in logarithmic expected time. ACM Trans. Math. Soft. 1977, 3(3), 209-226.
13. Sproull, R. F. Refinements to nearest-neighbor searching in kdimensional trees. Algorithmica 1991, 6, 579-589.
14. Omohundro, S. M. Bump trees for efficient function, constraint and classification learning. In Advances in Neural Information Processing Systems 3; Lippmann, Moody, Touretzky, Eds.; Morgan-Kaufmann: San Mateo, CA, 1991; pp 693-699.
15. Omohundro, S. M. Five balltree construction algorithms. International Computer Science Institute Technical Report TR-89-063, 1989, Berkeley, CA.
16. Samet, H. The quad-tree and related hierarchical data structures. ACM Comput. Surveys 1984, 16(2), 187-260.
17. Yanilos, P. Data structures and algorithms for nearest neighbor search in general metric spaces. In Proc. Fourth ACM-SIAM Sympos. Discrete Algorithms 1993, 311-321.
18. Agrafiotis, D. K.; Lobanov, V. S.; Rassokhin, D. R., paper in preparation.
19. Copyright 3-Dimensional Pharmaceuticals, Inc., 1994-1998.
20. Agrafiotis, D. K.; Lobanov, V. S, Salemme, F. R. patents pending.
21. Agrafiotis, D. K. On the use of information theory for assessing molecular diversity. J. Chem. Inf. Comput. Sci. 1997, 37(3), 576-580.
22. Lin, S. K. Molecular diversity assessment: logarithmic relations of information and species diversity and logarithmic relations of entropy and indistinguishability after rejection of Gibbs paradox of entropy mixing. Molecules 1996, 1, 57-67.
23. Snarey, M,; Terrett, N. K.; Willett, P.; Wilton, D. J. Comparison of algorithms for dissimilarity based compound selection. J. Mol. Graphics Mod., in press.
24. Mount, J.; Ruppert, J.; Welch, W.; Jain, A., IBC 6-th Annual Conference on Rational Drug Design; December 11 -12, 1996; Coronado, CA.
25. Waldman, M. Symposium on Diverse Perspectives of Molecular Diversity, ACS National Meeting, Dallas, TX, 1998.