RAPID: Randomized pharmacophore identification for drug design

Computational Geometry: Theory and Applications

Volumn 10, Issue 4, 1998, Pages 263-272

  Finn, P W ^a   Kavraki, L E ^c   Latombe, J C ^b   Motwani, R ^b   Shelton, C ^b   Venkatasubramanian, S ^b   Yao, A ^c  

^a PFIZER GLOBAL RESEARCH AND DEVELOPMENT   (United Kingdom)

^b Stanford University   (United States)

^c NONE

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0012418602     PISSN: 09257721     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0925-7721(98)00008-X     Document Type: Article

References (20)

1. T. Akutsu, H. Tamaki, T. Tokuyama, Distribution of distances and triangles in a point set and algorithms for computing the largest common point set, in: Proceedings of the ACM Symposium on Computational Geometry, Nice, France, 1997, pp. 314-322.
2. H. Alt, K. Mehlhorn, H. Wagener, E. Welzl, Congruence, similarity and symmetries of geometric objects, Discrete Comput. Geom. 3 (1988) 237-256.
3. K.S. Arun, T. Huang, S.D. Blostein, Least-squares fitting of two 3-d point sets, IEEE Trans. PAMI 9 (5) (1987) 698-700.
4. L. Balbes, S. Mascarella, D. Boyd, A perspective of modern methods in computer-aided drug design, in: K. Lipkowitz and D.B. Boyd, Eds., Reviews in Computational Chemistry, Vol. 5, VCH Publishers, 1994, pp. 337-370.
5. D. Barnum, J. Greene, A. Smellie, P. Sprague, Identification of common functional components among molecules, J. Chem. Inform. Comput. Sci. 36 (1997) 653-571.
6. D.B. Boyd, Aspects of molecular modeling, in: K. Lipkowitz and D.B. Boyd (Eds.), Reviews in Computational Chemistry, Vol. 1, VCH Publishers, 1990, pp. 321-351.
7. R. Brent, Algorithms for finding zeros and extrema of functions without calculating derivatives, Ph.D. Thesis, Stanford University, 1971.
8. G. Chang, W. Guida, W. Still, An internal coordinate Monte-Carlo method for searching conformational space, J. Amer. Chem. Soc. 111 (1989) 4379-4386.
9. P. Finn, D. Halperin, L. Kavraki, J.-C. Latombe, R. Motwani, C. Shelton, S. Venkatasubramanian, Geometric manipulation of flexible ligands, in: M. Lin and D. Manocha (Eds.), Lecture Notes in Computer Science, 1996 ACM Workshop on Applied Computational Geometry, Springer, Berlin, 1996, pp. 67-78.
10. P. Finn, L. Kavraki, J.-C. Latombe, R. Motwani, C. Shelton, S. Venkatasubramanian, A. Yao, Rapid: Randomized pharmacophore identification, in: Proceedings of the International Symposium on Computational Geometry, Nice, France, 1997, pp. 324-333.
11. A. Ghose, J. Kowalczyk, M. Peterson, A. Treasurywala, Conformational searching methods for small molecules: I. Study of the sybyl search method, J. Comput. Chem. 14 (9) (1993), 1050-1065.
12. T.F. Gonzalez, Clustering to minimize the maximum intercluster distance, Theor. Comput. Sci. 38 (1985) 293-306.
13. D. Halperin, C. Shelton, A perturbation scheme for spherical arrangements with application to molecular modeling, in: ACM Conference on Computational Geometry, Nice, France, 1997, pp. 183-192.
14. P. Indyk, R. Motwani, S. Venkatasubramanian, Geometric matching under noise: Combinatorial bounds and algorithms, Manuscript.
15. L.E. Kavraki, Random networks in configuration space for fast path planning, Ph.D. Thesis, Stanford University, 1995.
16. L.E. Kavraki, Geometry and the discovery of new ligands, in: J.-P. Laumond and M. Overmars (Eds.), Algorithms for Robotic Motion and Manipulation, A.K. Peters, 1997, pp. 435-448.
17. S. Khanna, R. Motwani, F.F. Yao, Approximation algorithms for the largest common set, Technical Report STAN-CS-95-1545, Stanford University, 1995.
18. A. Leach, A survey of methods for searching the conformational space of small and medium sized molecules, in: K. Lipkowitz and D. Boyd (Eds.), Reviews in Computational Chemistry, Vol. 2, VCH Publishers, 1991, pp. 1-47.
19. Y. Martin, M. Bures, E. Danaher, J. DeLazzer, I. Lico, A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists, J. Comput. Aided Molecular Design 7 (1993) 83-102.
20. P. Raghavan, S. Irani, Combinatorial and experimental results for randomized point algorithms, in: Proc. 12th ACM SCG, 1996, pp. 68-77.