Protein Structure Comparison and Visualization Tools on Cloud Platform
The biological function of a protein molecule is decided by its 3D-shape, which eventually determines how the molecule interacts with other molecules in living cells. Identifying similar structures between proteins provide the opportunity to recognize homology that is undetectable by sequence comparison. Thus comparison and alignment of protein structures represents a powerful means of discovering functions, yielding direct insight into the molecular mechanisms.
This paper proposes approaches in providing visualization tools for pairwise 3D protein structure alignment; our web service takes advantage of the Map Reduce paradigm as means of management and parallelizing tools under massive number of protein pairs examined under the experiment. It shows that our previously proposed sequential combinatorial algorithms are well parallelized under the map/reduce platform. These methods are tested on the real-world data obtained in from the RCSB PDB data set; the computation efficiency can be effectively improved proportional to the number of processors being used.
Keywordsprotein structures comparisons bioinformatics visualization VRML MapReduce Hadoop cloud computing
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- 1.Gerstein, M., Jansen, R., Johnson, T., Tsai, J., Krebs, W.: Motions in a data-base framework: from structure to sequence. In: Thorpe, M.F., Duxbury, P.M. (eds.) Rigidity Theory and Applications, pp. 401–442. Kluwer Academic/Plenum Publishers (1999)Google Scholar
- 4.Bujnicki, J.M.: Phylogeny of the restriction endonucleaselike superfamily inferred from comparison of protein structures. J. Mol. Evol. 50, 38–44 (2000)Google Scholar
- 6.Lin, Y.L., Lin, Y.H., Yu, P.S., Chang, H.C.: Randomized algorithms for three dimensional protein structures alignment. In: The 6th International Symposium on Computational Biology and Genome Informatics, pp. 122–125 (2005)Google Scholar
- 10.Lin, Y.L., Huang, S.P.: Tools and algorithms for refined comparison of protein structures. In: The 6th WSEAS International Conference on Microelectronics (MINO 2007), Istanbul, Turkey (2007)Google Scholar
- 11.Shin, H.S., Huang, S.P., Lin, Y.L.: Parametric searching algorithms with adaptive strategy for three dimensional protein structures alignments. In: National Computer Symposium (NCS 2007), Taichung, Taiwan, pp. 144–154 (2007)Google Scholar
- 12.Hadoop - Apache Software Foundation project home page, http://hadoop.apache.org/
- 13.Taylor, R.C.: An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics. BMC Bioinformatics 11, S1 (2010)Google Scholar
- 16.Martin, A.C.R., http://www.bioinf.org.uk/software/profit/
- 17.McLachlan, A.D.: Rapid comparison of protein structures. Acta Cryst. A38, 871–8783 (1982)Google Scholar
- 18.Euler, L.: Formulae generales pro trandlatione quacunque corporum rigidorum. Novi Acad. Sci. Petrop. 20, 189–207 (1775)Google Scholar
- 19.Gray, A.: A treatise on gyrostatics and rotational motion. MacMillan, London (1918)Google Scholar
- 22.Shin, H.S., Lin, Y.L., Jiang, W.D.: Protein structures alignment algorithms by parametric searching with trigonometric series. In: Proceedings of the 25th Workshop on Combinatorial Mathematics and Computation Theory, Hsinchu, Taiwan, pp. 44–54 (2008)Google Scholar
- 23.Chen, H.S., Lin, Y.L.: Comparisons of Semi-local Alignment Algorithms for Protein Structures. In: Proceedings of the 27th Workshop on Combinatorial Mathematics and Computation Theory (CMCT 2010), Taichung, Taiwan, April 30-May 1, pp. V6-254–V6-259 (2010)Google Scholar
- 24.Copyright (c) 1998 by Horst Vollhardt. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself (1998)Google Scholar
- 25.Chou, T.: Introduction to Cloud Computing: Business & TechnologyGoogle Scholar