PARS: a bioinformatic tool for Protein Assignment Regarding Secondary structure

Based on the statistical observation, sequence motifs have been introduced as regular patterns of amino acids that convey a specific structural or functional feature to a group of proteins. But, there is no report about the frequency distribution of the short lengths regularities (such as dipeptides) regarding its structural feature. To find a systematic view about the issue as mentioned above, we developed a bioinformatics tool, namely, PARS (Protein Assignment Regarding Secondary Structure), to enumerate all possible di- and tri-peptides in a given protein structure accompanied by assigning secondary structural elements for the first and second residues. This program can extract structural information of a PDB file, and determines the frequency distribution of 16 and 64 possible secondary structural of possible dipeptides and tripeptides respectively. It is implemented in C# programming language using the dynamic programming method. Using the structural files of a group of proteins, one can construct a detailed structural dataset for further analysis. Other applications include systems biology studies and logical designing of mutations. As an example, a brief description of the published article will be introduced at the end of this paper. This program is freely available for download at: http://www.znu.ac.ir/members/newpage/702/en