An Optimized Distance Function for Comparison of Protein Binding Sites
An important field of application of string processing algorithms is the comparison of protein or nucleotide sequences. In this paper we present an algorithm capable of determining the dissimilarity (distance) of protein sequences originating from protein binding sites found in the RS-PDB database that is a repaired and cleaned version of the publicly available Protein Data Bank (PDB). The special way of construction of these protein sequences enabled us to optimize the algorithm, achieving runtimes several times faster than the unoptimized approach. One example the algorithm proposed in this paper can be useful for is searching conserved sequences in protein chains.
KeywordsProtein Data Bank Protein Binding Site Substitution Matrice Protein Data Bank Entry Structure Protein Data Bank
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- 2.Grolmusz, V., Szabadka, Z.: Building a Structured PDB: The RS-PDB Database. In: Proc. of the 28th IEEE EMBS Annual International Conference, New York City, pp. 5755–5758. IEEE Computer Society Press, Los Alamitos (2006)Google Scholar
- 9.Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic Local Alignment Search Tool. Journal of Molecular Biology 215, 403–410 (1990)Google Scholar