engleski

Symbolic Cantor algorithm defines secondary protein structure of eukaryotes, prokaryotes and viruses

We present new computational algorithm for the secondary protein structure prediction. The method is named Symbolic Cantor Algorithm (SCA), and it is based on the symbolic dynamics and Cantor set coding of the nucleotide and amino acid addresses on the binary tree (Štambuk, N. (2000) Croat. Chem. Acta 73, 1123). The algorithm has two steps. Protein or gene sequence is first transformed into a numerical series of the symbolic coding addresses. The second step of the model involves the extraction of the rules for the recognition of particular folding type by means of the machine learning and spectral analyses of different string parameters. The method was tested on nonhomologous alpha- and beta-protein folds obtained from the Jpred database. It is shown that SCA enables quick, simple and accurate prediction of the secondary protein folding types on a personal computer.

amino acids; Cantor; coding; computational algorithm; eukaryotes; machine learning; nucleotides; prokaryotes; protein folding; structure; viruses

nije evidentirano