Approximation algorithms for 3-D common substructure identification in drug and protein molecules

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 1663, Issue , 1999, Pages 253-264

  Chakraborty, Samarjit ^a   Biswas, Somenath ^b  

^a ETH ZURICH   (Switzerland)

^b INDIAN INSTITUTE OF TECHNOLOGY KANPUR   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DATA STRUCTURES; GEOMETRY; MOLECULAR BIOLOGY; MOLECULES; PATTERN MATCHING; PROTEINS;

APPROXIMATION RATIOS; BIPARTITE GRAPHS; DECISION ALGORITHMS; GEOMETRIC PATTERN MATCHING; GUARANTEED APPROXIMATION RATIOS; MAXIMUM MATCHINGS; PROTEIN MOLECULES; THREE DIMENSIONS;

APPROXIMATION ALGORITHMS;

EID: 34247094868     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/3-540-48447-7_26     Document Type: Conference Paper

References (17)

1. Proc. 12th. Annual ACM Symp. on Computational Geometry, 1996.
2. Proc. 3rd. Annual Intl. Conf. on Computational Molecular Biology, April, 1999.
3. T. Akutsu. Protein structure alignment using dynamic programming and iterative improvement. IEICE Trans. Information and Systems, E79-D:1629-1636, 1996.
4. T. Akutsu, H. Tamaki, and T. Tokuyama. Distribution of distances and triangles in a point set and algorithms for computing the largest common point sets. Discrete and Computational Geometry, 20:307-331, 1998.
5. S. Arya, D. M. Mount, N. S. Netanyahu, R. Silverman, and A. Wu. An optimal algorithm for approximate nearest neighbor searching. In Proc. 5th. Annual ACM-SIAM Symp. on Discrete Algorithms, pages 573-582, 1994.
6. S. Chakraborty and S. Biswas. Approximation algorithms for 3-D common substructure identification in drug and protein molecules. Technical Report TIK Report No. 69, Eidgenössische Technische Hochschule Zürich, 1999. ftp://ftp.tik.ee.ethz.ch/pub/people/samarjit/paper/CB99a.ps.gz.
7. L. P. Chew, K. Kedem, J. Kleinberg, and D. Huttenlocher. Fast detection of common geometric substructure in proteins. In Proc. RECOMB'99-3rd. Annual International Conference on Computational Molecular Biology [2].
8. A. Efrat and A. Itai. Improvements on bottleneck matching and related problems using geometry. In Proc. 12th. Annual ACM Symp. on Computational Geometry [1], pages 301-310.
9. P. W. Finn, L. E. Kavraki, J-C. Latombe, R. Motwani, C. Shelton, S. Venkata-Subramanian, and A. Yao. RAPID: Randomized pharmacophore identification for drug design. In Proc. 13th. Annual ACM Symp. on Computational Geometry, pages 324-333, Centre Universitaire Méditerranéen, Nice, France, 1997.
10. D. Fischer, R. Nussinov, and H. J. Wolfson. 3-D substructure matching in protein molecules. In Proc. 3rd. Annual Symposium on Combinatorial Pattern Matching, April 1992. LNCS 644, pages 136-150.
11. M. T. Goodrich, J. S. B. Mitchell, and M. W. Orletsky. Practical methods for approximate geometric patern matching under rigid motions. In Proc. 10th. Annual ACM Symp. on Computational Geometry, pages 103-112, 1994.
12. J. Hopcroft and R. M. Karp. An n5/2 algorithm for maximum matchings in bipartite graphs. SIAM J. Computing, 2:225-231, 1973.
13. P. Indyk, R. Motwani, and S. Venkatasubramanian. Geometric matching under noise: Combinatorial bounds and algorithms. In Proc. 10th. Annual ACM-SIAM Symp. on Discrete Algorithms, 1999.
14. S. Irani and P. Raghavan. Combinatorial and experimental results for randomized point matching algorithms. In Proc. 12th. Annual ACM Symp. on Computational Geometry [1], pages 68-77.
15. S. Lavalle, P. Finn, L. Kavraki, and J-C. Latombe. Efficient database screening for rational drug design using pharmacophore-constrained conformational search. In Proc. RECOMB'99-3rd. Annual International Conference on Computational Molecular Biology [2].
16. K. Mehlhorn. Data Structures and Algorithms 3: Multi-dimensional Searching and Computational Geometry. Springer Verlag, Berlin, 1984.
17. S. Schirra. Approximate decision algorithms for approximate congruence. Information Processing Letters. 43:29-34, 1992.