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Simulation peptide toxicity using the fragments of local symmetry in amino acid sequences
Andrey A Toropov1, Alla P Toropova1, Valentin O Kudyshkin2
1Department of Environmental Health Science, Laboratory of Environmental Chemistry and Toxicology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy.
Abstract:
An efficient scheme for modeling peptide toxicity is proposed and applied. The peptide cytotoxicity is calculated in the form of a mathematical function of its constituent amino acids, represented by single-symbol abbreviations. It was found that considering the so-called fragments of local symmetry can significantly increase the predictive potential of the proposed models. The best model gives for validation set value of Matthews correlation coefficient 0.7 on the set of 2784 peptides. The prospects for applying the ideas of infodynamics to research activities related to modeling the biochemical behavior of peptides are discussed.
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