Abstract
Features of newly emerging protein structure data are very large, extremely complex and multi dimensional. Furthermore, it is complicated to manage structural information with flat file for comparison and prediction of protein structure. Therefore, it is necessary to make a model of protein structures to store them into database and to represent spatial arrangements and topological relationships for providing analysis applications of protein structures with structural information.
This paper describes extracting structural features from flat file, making a model protein structures based on a network spatial model and querying relationships among protein structures using topological and geometric operators. Existing spatial DBMS can store and retrieve spatial features of protein structures with spatial index by protein structure modeling using spatial types.
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References
Han, Y., Park, S.H., Ryu, K.H.: Modeling of three Dimensional Structure in Protein based on Spatial Object Model. Proc. of Korea Info. Sci. Soc. 29(1), 73–75 (2002)
Rigaus, P., School, M., Voisard, A.: Spatial Databases with application to GIS, pp. 29–61. Academic Press, San Diego (2002)
Oracle Spatial User’s Guide and Reference: Loading and Indexing Spatial Object Types. Release 8.1.5, Oracle (2001)
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data bank. J. Nucleic Acids Research 28, 235–242. Oxford University Press, New York (2002)
Higgins, D., Tailor, W.: Bioinfomatics: Sequence, Structure, and databanks, 1st edn. Oxford University Press, New York (2000)
Ryu, K.H.: Genome database & EST database. J. Scientific & Technological Knowledge Infrastructure 10 KORDIC, 48–61 (2000)
Holm, L., Sander, C.: Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Research 25, 231–234. Oxford University Press, New York (1997)
Levitt, M.: Competitive assessment of protein fold recognition and alignment accuracy. Int. J. Proteins Struct. Funct. Genet. 1, 92–104 (1997)
Stultz, M., Nambudripad, R., Lathrop, H., White, V.: Predicting protein structure with probabilistic models. Int. J. Adv. Mol. Cell Biol. 22B, 447–506 (1997)
Alexandrov, N., Nussinov, R.: Fast Protein fold recognition via sequence to structure alignment and contact capacity protentials. In: Proc. of Pac. Symp on Biocomput., pp. 53–72 (1996)
Garnier, J., Gibrat, J.-F., Robson, B.: GOR method for predicting protein secondary structure from amino acid sequence. J. Method Enzymol. 266, 540–553 (1996)
Johnson, M.S., May, A.C., Ridionov, M.A., Overington, J.P.: Discrimination of common protein folds: Application of protein structure to sequence/structure comparisons. J. Methods Emzymol. 266, 575–598 (1996)
Clementini, E., Felice, P., van Oostrom, P.: A small set of formal topological relationships suitable for end-user interaction. In: Proc. of Spatial Databases Symp., Singapore, pp. 277–295 (1993)
Altschul, S.F., Carrol, R.J., Lipman, D.J.: Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990)
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Park, SH., Ryu, K.H., Son, H.S. (2003). Protein Structure Modeling Using a Spatial Model for Structure Comparison. In: Liu, J., Cheung, Ym., Yin, H. (eds) Intelligent Data Engineering and Automated Learning. IDEAL 2003. Lecture Notes in Computer Science, vol 2690. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-45080-1_68
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DOI: https://doi.org/10.1007/978-3-540-45080-1_68
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