Online Programs and Databases of Peptides and Proteolytic Enzymes – A Brief Update for 2007–2008
Piotr Minkiewicz, Jerzy Dziuba*, Małgorzata Darewicz, Anna Iwaniak and Justyna Michalska
University of Warmia and Mazury in Olsztyn, Chair of Food Biochemistry, Plac Cieszyński 1, PL-10-726 Olsztyn-Kortowo, Poland
Article history:
Received April 21, 2009
Accepted June 17, 2009
Key words:
peptides, peptidomics, proteolysis, bioinformatics, computer databases, world wide web
Summary:
Bioinformatics methods have become one of the most important tools in peptide science. The number of available peptide databases is growing rapidly. The number of online programs able to process peptide sequences to extract information concerning their structure, physicochemical and biological properties is also increasing. Many of such programs were designed to manipulate protein sequences, but they have no built-in restrictions disabling their application to process oligopeptides containing less than 20 amino acid residues. Publications addressing these programs cannot be found in literature databases using the keyword 'peptide' or 'peptides', in connection with the term 'bioinformatics' or related terms, thus a reference source summarizing data from such publications seems necessary. This paper provides a brief review of bioactive peptide databases and sequence alignment programs enabling the search for peptide motifs, determination of physicochemical properties of amino acid residues, prediction of peptide structure, the occurrence of posttranslational glycosylation and immunogenicity, as well as the support of peptide design process. The review also includes databases and programs providing information about proteolytic enzymes. The databases and programs discussed in this paper were developed or updated between September 2007 and December 2008.
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