An optimized distance function for comparison of protein binding sites

  • Authors:

  • Gábor Iván

  • Affiliations:

  • Department of Computer Science, Eötvös University, Budapest, Hungary

  • Venue:
  • BSB'07 Proceedings of the 2nd Brazilian conference on Advances in bioinformatics and computational biology
  • Year:
  • 2007

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Abstract

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.