Towards index-based similarity search for protein structure databases

Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

Volumn , Issue , 2003, Pages 148-158

  Camoglu O ^a   Kahveci, T ^a   Singh, A K ^a  

^a University of California   (United States)

Author keywords

dataset join; feature vectors; indexing; Protein structures

Indexed keywords

BIOINFORMATICS; INDEXING (OF INFORMATION);

FEATURE VECTORS; MULTI-DIMENSIONAL INDEX STRUCTURES; PAIRWISE ALIGNMENT; PROTEIN STRUCTURE DATABASE; PROTEIN STRUCTURES; SECONDARY STRUCTURE ELEMENTS; SIMILARITY SEARCH; STATISTICAL MODELING;

PROTEINS;

EID: 84960463924     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CSB.2003.1227314     Document Type: Conference Paper

References (23)

1. http://www.rcsb.org/pdb/.
2. http://alto.rockefeller.edu/modbase-cgi/index.cgi.
3. N.N. Alexandrov and D. Fischer. Analysis of topological and nontopological structural similarities in the PDB: new examples from old structures. Proteins, 25:354-365, 1996.
4. Mihael Ankerst, Gabi Kastenmüller, Hans-Peter Kriegel, and Thomas Seidl. Nearest neighbor classification in 3D protein databases. In 34-43, 1999.
5. K.S. Arun, T.S. Huang, and S.D. Blostein. Least-squares fitting of two 3-D point sets. IEEE Transactions on Pattern Analysis and Machine Intelligence, PAMI-9(5):698-700, September 1987.
6. N. Beckmann, H.-P. Kriegel, R. Schneider, and B. Seeger. The R∗-tree: An efficient and robust access method for points and rectangles. In SIGMOD, pages 322-331, Atlantic City, NJ, 1990.
7. O. Çamoğlu, T. Kahveci, and A. Singh. PSI: Indexing protein structures for fast similarity search. In ISMB, 2003.
8. I. Eidhammer and I. Jonassen. Protein structure comparison and structure patterns - an algorithmic approach. ISMB tutorial, 2001.
9. H. Gabow. Implementation of Algotihms for Maximum Matching on Nonbipartite Graphs. PhD thesis, Stanford University, 1973.
10. M. Gerstein and M. Levitt. Using iterative dynamic programming to obtain pairwise and multiple alignments of protein structures. In ISMB, pages 59-66, 1996.
11. L. Holm and C. Sander. Protein structure comparison by alignment of distance matrices. Journal of Molecular Biology, 233:123-138, 1993.
12. L. Holm and C. Sander. 3-D lookup: Fast protein structure database searches at 90 % reliability. In ISMB, pages 179-187, 1995.
13. I. Koch, T. Lengauer, and E. Wanke. An algorithm for finding maximal common subtopologies in a set of protein structures. Journal of Computational Biology, 3(2):289-306, 1996.
14. T. Madej, J.-F. Gibrat, and S.H. Bryant. Threading a database of protein cores. Proteins, 23:356-369, 1995.
15. K. Mizguchi and N. Go. Comparison of spatial arrangements of secondary structural elements in proteins. Protein Engineering, 8:353-362, 1995.
16. R. Nussinov and H.J. Wolfson. Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc. National Academy of Sciences of the USA, pages 10495-10499, 1991.
17. R. Ramakrishnan and J. Gehrke. Database Management Systems. MC Graw Hill, 2000.
18. S.D. Rufino and T.L. Blundell. Structure-based identification and clustering of protein families and superfamilies. Journal of Computer Aided Molecular Design, 8:5-27, 1994.
19. H.N. Shindyalov and P.E. Bourne. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering, 11(9):739-747, 1998.
20. A.P. Singh and D.L. Brutlag. Hierarchical protein structure superposition using both secondary structure and atomic representations. In ISMB, pages 284-293, 1997.
21. W.R. Taylor. Protein structure comparison using iterated double dynamic programming. Protein Science, 8:654-665, 1999.
22. W.R. Taylor and C.O. Orengo. Protein structure alignment. Journal of Molecular Biology, 208:1-22, 1989.
23. H.J. Wolfson and I. Rigoutsos. Geometric hashing: An introduction. IEEE Computational Science & Engineering, pages 10-21, Oct-Dec 1997.