Rapid protein fragment search using hash functions based on the fourier transform

Bioinformatics

Volumn 13, Issue 4, 1997, Pages 357-364

  Akutsu, Tatsuya ^a   Onizuka, Kentaro ^b   Ishikawa, Masato ^c  

^a UNIVERSITY OF TOKYO   (Japan)

^b Matsushita Research Institute Tokyo Inc   (Japan)

^c MEIJI UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DATA BASE; FOURIER TRANSFORMATION; PRIORITY JOURNAL; PROTEIN STRUCTURE;

ALGORITHMS; COMPUTERS; DATABASES, FACTUAL; EVALUATION STUDIES; FOURIER ANALYSIS; PEPTIDE FRAGMENTS; PROTEINS; SEQUENCE ALIGNMENT;

EID: 0030850641     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/13.4.357     Document Type: Article

References (15)

1. Akutsu.T. (1994) Efficient and robust three-dimensional pattern matching algorithms using hashing and dynamic programming techniques. In Proceedings of the 28th Hawaii International Conference on System Sciences. IEEE Computer Society Press, Los Alamitos, CA, Vol. 5, pp. 225-234.
2. Bernstein, F., Koetzle.T., Williams, G., Meyer.E., Brice.M., Rodgers.J.. Kennard.O., Shimanouchi.T. and Tasumi.M. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112,535-542.
3. Crippen, G.M. and Maiorov.V.N (1995) How many protein folding motifs are there? J. Mol. Biol., 252, 144-151.
4. Holm.L. and Sander.C. (1995) 3-D Lookup: fast protein structure database searches at 90% reliability. In Proceedings of an International Conference on Intelligent Systems for Molecular Biology. AAAI Press. Menlo Park, CA, pp. 179-187.
5. Holm.L., Onzounis.C. Sander.C., Tuparev.G. and Vriend.G. (1992) A database of protein structure families with common folding motifs. Protein Sci., 1, 1691-1698.
6. Kalvin, A., Schonberg, E., Schwartz, I.T. and Sharir, M. (1986) Two-dimensional, model-based, boundary matching using footprints. Int. J. Robotics Res., 5, 28-55.
7. Kishon.E. and Wolfson.H. (1987) 3-D curve matching. In Proceedings of the AAAI Workshop on Spatial Reasoning and Multi-Sensor Fusion. AAAI Press, Menlo Park. CA, pp. 250-261.
8. Nussinov, R. and Wolfson.H.J. (1991) Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc. Natl Acad. Sci. USA, 88, 10495-10499.
9. Onizuka.K., Asai.K., Ishikawa.M. and Wong.S.T.C. (1993) A multi-level description scheme of protein conformation. In Proceedings of an International Conference on Intelligent Systems in Molecular Biology. AAAI Press, Menlo Park, CA, pp. 301-310.
10. Pascarella.S. and Argos.P. (1992) A data bank merging related protein structures and sequences. Protein Eng., 5, 121-137.
11. Pearson.W.R. and Lipman.D.J. (1988) Improved tools for biological sequence comparison, Proc. Natl Acad. Sci. USA, 85, 2444-2448.
12. Rao.S.T. and Rossmann.M.G. (1973) Comparison of super-secondary structures in proteins. J. Mol. Biol., 76, 241-256.
13. Schwartz.J.T. and Sharir.M. (1987) Identification of partially obscured objects in two and three dimensions by matching noisy characteristic curves. Int. J. Robotics Res.. 6, 29-44.
14. Taylor.W.R. and Orengo.C.A. (1989) Protein structure alignment. J. Mol. Biol., 208, 1-22.
15. Willard.D.E. (1985) New data structures for orthogonal range queries. SIAM J. Comput., 14, 232-253.