Protein structure alignment using dynamic programming and iterative improvement

IEICE Transactions on Information and Systems

Volumn E79-D, Issue 12, 1996, Pages 1629-1636

  Akutsu, Tatsuya ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

Alignment; Bio informatics; Computational geometry; Geometric pattern matching; Protein structure

Indexed keywords

APPROXIMATION THEORY; COMPUTATIONAL COMPLEXITY; COMPUTATIONAL GEOMETRY; DYNAMIC PROGRAMMING; ITERATIVE METHODS; MOLECULAR STRUCTURE; SAMPLING; THREE DIMENSIONAL;

GEOMETRIC PATTERN MATCHING PROBLEM; PROTEIN STRUCTURE ALIGNMENT;

ALGORITHMS;

EID: 0030377824     PISSN: 09168532     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (19)

1. T. Akutsu, Efficient and robust three-dimensional pattern matching algorithms using hashing and dynamic programming techniques, Proc. 27th Hawaii International Conference on System Sciences, vol.5, pp.225-234, 1994.
2. T. Akutsu, Substructure search and alignment algorithms
3. for three-dimensional protein structures, Research Report 94-AL-41-1, pp.1-8, Information Processing Society of Japan, 1994.
4. F.C. Bernstein, T.F. Koetzle, G.J. B. Williams, E.F. Meyer Jr., M.D. Brice, J.R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi, The Protein Data Bank: A computer-based archival file for macromolecular structures, J. Molecular Biology, vol.112, pp.535-542, 1976.
5. C. Branden and J. Tooze, Introduction to Protein Structure, Garland Publishing, New York, 1991.
6. D. Eppstein, Z. Galil, R. Giancarlo, and G.F. Italiano, Sparse dynamic programming I: linear cost functions, J. ACM, vol.39, pp.519-545, 1992.
7. M.T. Goodrich, J.S.B. Mitchell, and M.W. Orletsky, Practical methods for approximate geometric pattern matching under rigid motions, Proc. 10th ACM Symp. Computational Geometry, pp.103-112, 1994.
8. L. Holm, C. Onzounis, C. Sander, G. Tuparev, and G. Vriend, A database of protein structure families with common folding motifs, Protein Science, vol.1, pp.1691-1698, 1992.
9. L. Holm and C. Sander, 3-D lookup: fast protein structure database searches at 90% reliability, Proc. 3rd International Conference on Intelligent Systems for Molecular Biology (ISMB'95), pp.179-187, 1995.
10. A.M. Lesk, Protein Architecture: A Practical Approach, IRL Press, New York, 1991.
11. R. Nussinov and H.J. Wolfson, Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques, Proc. Natl. Acad. Sci. (USA), vol.88, pp.10495-10499, 1991.
12. C.A. Orengo, D.T. Jones, and J.M. Thornton, Protein superfamilies and domain superfolds, Nature, vol.372, pp.631-634, 1994.
13. S. Pascarella and P. Argos, A data bank merging related protein structures and sequences, Protein Engineering, vol.5, pp. 121-137, 1992.
14. F.P. Preparata and M.I. Shamos, Computational Geometry: an Introduction, Springer-Verlag, 1985.
15. S.T. Rao and M.G. Rossmann, Comparison of supersecondary structures in proteins, J. Molecular Biology, vol.76, pp.241-256, 1973.
16. A. Šali and J.P. Overington, Derivation of rules for comparative protein modeling from a database of protein structure alignments, Protein Science, vol.3, pp.1582-1596, 1994.
17. S. Schirra, Approximate decision algorithms for approximate congruence, Information Processing Letters, vol.43, pp.29-34, 1992.
18. W.R. Taylor and C.A. Orengo, Protein structure alignment, J. Molecular Biology, vol.208, pp.1-22, 1989.
19. G. Vriend and C. Sander, Detection of common three-dimensional substructures in proteins, PROTEINS: Structure, Function, and Genetics, vol.11, pp.52-58, 1991.