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QSAR modeling of endpoints for peptides which is based on representation of the molecular structure by a sequence of amino acids

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Abstract

The representation of the molecular structure by a system (sequence) of amino acids has been used to establish quantitative structure–property/activity relationships (QSPR/QSAR) which can be used for (i) bioactivities of epitope-peptides, (ii) antibacterial potencies of polypeptides, and (iii) the binding affinity of peptides that bind to the class I major histocompatibility complex molecule HLA-A*0201. The representation of the peptide structure has been done via 1-letter abbreviations of amino acids, i.e., A (alanine), C (cysteine), D (aspartic), etc. This approach allows classifying amino acids according to their function in a biochemical process (promoters of increase or decrease of an endpoint).

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Acknowledgments

The authors express their gratitude to ANTARES (the project number LIFE08-ENV/IT/00435) for financial support. Also the authors would like to express their gratitude to J. Baggott for English editing.

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Authors and Affiliations

  1. Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156, Milan, Italy

    Andrey A. Toropov, Alla P. Toropova & Emilio Benfenati

  2. 3rd Department of Medicine—Department of Endocrinology and Metabolism, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, U Nemocnice 1, 12808, Prague 2, Czech Republic

    Ivan Raska Jr.

  3. Department of Electronics and Information, Politecnico di Milano, Via Ponzio 34/5, 20133, Milan, Italy

    Giuseppina Gini

Authors
  1. Andrey A. Toropov
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  2. Alla P. Toropova
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  3. Ivan Raska Jr.
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  4. Emilio Benfenati
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  5. Giuseppina Gini
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Correspondence to Andrey A. Toropov.

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Toropov, A.A., Toropova, A.P., Raska, I. et al. QSAR modeling of endpoints for peptides which is based on representation of the molecular structure by a sequence of amino acids. Struct Chem 23, 1891–1904 (2012). https://doi.org/10.1007/s11224-012-9995-0

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  • DOI: https://doi.org/10.1007/s11224-012-9995-0

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