3D-BLAST: 3D protein structure alignment, comparison, and classification using spherical polar fourier correlations

Pacific Symposium on Biocomputing 2010, PSB 2010

Volumn , Issue , 2010, Pages 281-292

  Mavridis, Lazaros ^a   Ritchie, David W ^a  

^a LORIA   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTERING APPROACH; DATABASE QUERIES; DATABASE SEARCHES; FOURIER; HIGH PRECISION; NO REDUCTION; PLOT ANALYSIS; PROTEIN SHAPE; PROTEIN STRUCTURE ALIGNMENT; PROTEIN STRUCTURES; TIME-SCALES;

PROTEINS; QUERY LANGUAGES; SEARCH ENGINES; THREE DIMENSIONAL COMPUTER GRAPHICS;

THREE DIMENSIONAL;

PROTEIN;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; COMPUTER PROGRAM; FOURIER ANALYSIS; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN DOMAIN; STRUCTURAL HOMOLOGY;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; FOURIER ANALYSIS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEINS; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 79960775974     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (32)

1. L. Holm and C. Sander. Trends in Biochemical Sciences. 20, 478 (1995).
2. H.M. Berman et al. Acta Cryst. D58, 899 (2002).
3. R. Kolodny, P. Koehl, and M. Levitt. J. Mol. Biol. 346, 1173 (2005).
4. E. Krissinel and K. Henrick. Proceedings of the Fifth international Conference on Molecular Structural Biology, Vienna. 88 (2003).
5. I.N. Shindyalov and P.E. Bourne. Protein Engineering 11, 739 (1998).
6. T. Madej, J.F. Gibrat and S.H. Bryant. Proteins: Struct, Func. Bioinf. 23, 356 (1995).
7. M.J. Sippl and M. Widerstein. Bioinformatics. 24, 426 (2008).
8. A.L. Cuff, I. Sillitoe, T. Lewis, O.C. Redfern, R. Garratt, J. Thornton, and C.A. Orengo. Nucleic Acids Research. 37, 310 (2008).
9. A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia. J. Mol. Biol. 247, 536 (1995).
10. C.A. Orengo and W.R. Taylor. Methods Enzymol. 266, 617 (1996).
11. L. Mak, S. Grandison, and R.J. Morris. J. Mol. Graph. Model. 26, 1035 (2008).
12. L. Sael, B. Li, D. La, Y. Fang, K. Ramani, R. Rustamov, and D. Kihara. Proteins: Struct, Func. Bioinf. 72, 1259 (2008).
13. M. Novotni and R.J. Klein. J. Comp.-Aided Mol. Des. 36, 1047 (2004).
14. D.W. Ritchie and G.J.L. Kemp. Proteins: Struc., Funct., Genet. 39, 178 (2000).
15. D.W. Ritchie, D. Kozakov, and S. Vajda. Bioinformatics. 24, 1865 (2008).
16. S.E. Leicester, J. L. Finney and R.P. Bywater, JMG. 6, 104 (1988).
17. S.E. Leicester, J. Finney and R. Bywater. J. Math. Chem. 16(3-4), 315 (1994).
18. S.E. Leicester, J. Finney and R. Bywater. J. Math. Chem. 16(3-4), 343 (1994).
19. N.L. Max and E.D. Getzoff. IEEE Comput. Graphics Appl. 8(4), 42 (1988).
20. N.L. Max. JMG. 6(4) 210 (1988).
21. B.S. Duncan and A.J. Olson. Biopolymers. 33, 219 (1993).
22. B.S. Duncan and A.J. Olson. Biopolymers. 33, 231 (1993).
23. B.S. Duncan and A.J. Olson. JMG. 13, 258 (1995).
24. B.S. Duncan and A.J. Olson. JMG. 13, 250 (1995).
25. A. Gramada and P.E. Bourne, BMC Bioinformatics, 7, 242 (2006).
26. R.J. Morris, R.J. Najmanovich, A. Kahraman and J.M. Thornton, Bioinformatics, 21(10), 2347 (2005).
27. D.W. Ritchie. J. Appl. Cryst. 38, 808 (2005).
28. J.P. Egan. Academic Press, New York (1975).
29. L. Mavridis, B.D. Hudson and D.W. Ritchie, J. Chem. Inf. Model., 47(5), 1787 (2007).
30. M. Gerstein and M. Levitt, Protein Science. 7(2), 445 (1998).
31. A.D. McLachlan. Acta Cryst. A38, 871 (1982).
32. J.H. Ward. J. Am. Stat. Assoc. 58(301), 236 (1963).