Aligning multiple protein structures by deterministic annealing

Journal of Bioinformatics and Computational Biology

Volumn 3, Issue 4, 2005, Pages 837-860

  Zhou, Tianshou ^a   Chen, Luonan ^b   Tang, Yun ^c   Zhang, Xiangsun ^d  

^a SUN YAT SEN UNIVERSITY   (China)

^b OSAKA SANGYO UNIVERSITY   (Japan)

^c TSINGHUA UNIVERSITY   (China)

^d INSTITUTE OF APPLIED MATHEMATICS   (China)

Author keywords

Alignment; Annealing; Mean field; Mixed integer programming; Permutation; Protein structure

Indexed keywords

ABC TRANSPORTER; ACYLTRANSFERASE; ALDEHYDE DEHYDROGENASE;

ARTICLE; CONTROLLED STUDY; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; PREDICTION; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN STRUCTURE; SIMULATION; STRUCTURE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTER SIMULATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUMERICAL ANALYSIS, COMPUTER-ASSISTED; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 22544439648     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720005001351     Document Type: Article

References (27)

1. Holm L, Sander C, Protein structure comparison by alignment of distance matrices, J Mol Biol 233:123-138, 1993.
2. Shindyalov I, Bourne P, Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Eng 11:739-747, 1998.
3. Gerstein M, Levitt M, Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures, Proceedings of the Fourth International Conference on Intelligent Systems in Molecular Biology (ISMB), 59-67, 1996.
4. Bryant SH, Altschul SF, Statistics of sequence-structure threading, Curr Opin Struc Biol 5:236-244, 1995.
5. Chen L, Zhou T, Tang Y, Protein structure alignment by deterministic annealing, Bioinformatics 21:51-62, 2004.
6. Blankenbecler R, Ohlsson M, Peterson C, Ringner M, Matching protein structures with fuzzy alignments, Proceedings of the National Academy of Sciences 100, pp. 11936-11940, 2003.
7. Haraldsson H, Ohlsson M, A fuzzy matching approach to multiple structure alignment of proteins, LU TP 03-17, (http://www.thep.lu.se/tf2/complex/), 2003.
8. Hiroike T, Toh H, A local structural alignment method that accommodates with circular permutation, Chem-Bio Informatics Journal 1:739-747,(3):103-114, (3):103-114, 2001.
9. Guda C, Scheeff E, Bourne P, Shindyalov I, A new algorithm for the alignment of multiple protein structures using Monte Carlo optimization, Proceedings of the Pacific Symposium on Biocomputing 6, pp. 275-286, 2001.
10. Orengo CA, Taylor WR, SSAP: Sequential structure alignment program for protein structure comparison, Methods Enzymol 266:617-635, 1996.
11. Leibowitz N, Fligeman ZY, Nussinov R, Wolfson HJ, Automated multiple structure alignment and detection of a common substructure motif, Proteins 43:235-245, 2001.
12. Szustakowski J, Weng Z, Structural alignment using a genetic algorithm, Proteins 38:438-440, 2000.
13. Mount DW, Bioinformatics, Cold Spring Harbor Laboratory Press, 2001.
14. Zhang X, Wang Y, Zhan Z, Wu L, Chen L, Exploring protein's optimal HP configurations by self-organizing mapping, Journal of Bioinformatics and Computational Biology 3:385-400, 2005.
15. Peterson C, Anderson JR, A mean field theory learning algorithm for neural networks, Complex Systems 1:995-1019, 1987.
16. Peterson C, Soderberg B, A new method for mapping optimization problems onto neural networks, Int J Neural Sys 1:3-22, 1989.
17. Chen L, Aihara K, Chaotic simulated annealing by a neural network model with transient chaos, Neural Networks 8(6):915-930, 1995.
18. Chen L, Aihara K, Chaos and asymptotical stability in discrete-time neural networks, Physica D 104:286-325, 1997.
19. Nemhauser GL, Wolsey LA, Integer and Combinatorial Optimization, New York, Wiley, 1988.
20. Bazaraa MS, Sherali HD, Shetty CM, Nonlinear Programming: Theory and Algorithms, 2nd ed., Wiley, New York, 1993.
21. Luenberger DG, Linear and Nonlinear Programming, 2nd ed., Kluwer Academic Publishers, 2003.
22. Urahama K, Analog method for solving combinatorial optimization problems, IEICE T Inf Sys (The Institute of Electronics, Information and Communication Engineers) E77-A:302-308, 1994.
23. Ishii S, Sato M, Doubly constrained network for combinatorial optimization, Neurocomputing 43:239-257, 2002.
24. Arun KS, Huang TS, Blostein SD, Least-squares fitting of two 3-D point sets, IEEE Pattern Anal PAMI-9(5):698-701, 1987.
25. Higham NJ, Newton's method for the matrix square root, Math Comput 46(174): 537-549, 1986.
26. Neumann JV, Some matrix-inequalities and metrization of matric-space, Tomsk Uni Rev 1:286-300, 1937.
27. Mizuguchi K, Deane CM, Blundell TL, Overington JP, HOMSTRAD: A database of protein structure alignments for homologous families, Protein Science 7:2469-2471, 1998.