Effective filtering for structural similarity search in protein 3D structure databases

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

Volumn 3180, Issue , 2004, Pages 761-770

  Park, Sung Hee ^a   Ryu, Keun Ho ^a  

^a Chungbuk National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL PROPERTIES; DATABASE SYSTEMS; EXPERT SYSTEMS; GRAPHIC METHODS; TOPOLOGY;

DISTANCE FUNCTIONS; FILTERING METHOD; PROTEIN 3-D STRUCTURE; SEQUENCE COMPARISONS; SIMILARITY SEARCH; SPATIAL FEATURES; STRUCTURAL ALIGNMENTS; STRUCTURAL SIMILARITY;

PROTEINS;

EID: 33746221755     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-30075-5_73     Document Type: Article

References (12)

1. L. Holm, C. Sander Proein structure comparison by alignment of distance matrices, J. of Mol. Biol., Vol. 233. (1993) 123-138
2. C.A. Orengo, W.R. Taylor. SSAP: Sequential structure alignment program for protein structure comparison. J. of Methods in Enzym., Vol.266. (1996) 617.635
3. I. N. Shindyalov, P.E. Bourne: Protein structure alignment by incremental combinatorial extension of the optimal path, Protein Eng., Vol.11. (1998) 739-747
4. N. Alexandrov, D. Fisher: Analysis of topological and nontopological structural similarities in the PDB: New examples with old structures, Protein, Vol.25.(1996) 354-365
5. I. Koch, T. Lengauer, E. Wanke: An algorithm for finding maximal common subtopologies in asset of protein structures,. J. comput. Biol., Vol.3.(1996) 289-306
6. D. Gilbert, D.R. Westhead, N. Nagano, J.M. Thornton: Motif-based searching in TOPS protein topology databases.,J. of Bioinformatics, Vol. 15. Oxford University Press New York (1999) 317-326
7. J.-F. Gibrat, T. Madej, H. Bryant: Surprising similarities in structure comparison, Current Opinion in Structural Biology, Vol. 6 (1996) 377-385
8. Guttman: A. R-Trees: A Dynamic Index Structure for Spatial Searching, In Proc. ACM SIGMOD Intl. Symp. on the Management of Data(1984) 45-47
9. E. Clementini, P. Felice, P. van Oostrom: A small set of formal topological relationships suitable for end-user interaction. In: Proc. of Spatial Databases Symp., Singapore (1993) 277-295
10. Amit P. Singh, Douglas L. Brutlag: Protein Structure Alignment: A Comparison of Methods, Dept. of Biochemistry, Stanford Univ (2000)
11. L. Holm, J. Park: DaliLite workbench for protein structure comparison, Bioinformatics. Vol. 16. Oxford University Press New York (2000) 566-567
12. S.H. Park, K.H. Ryu, H.S. Son: Modeling Protein Structures with Spatial Model for Structure Comparison, LNCS, Vol. 2690. Springer-Verlag Berlin Heidelberg .(2003) 490-497