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Protein structure discovery: A software package to computer proteomics tasks (Review)

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Abstract

A software information system called Protein Structure Discovery was developed. The system can be used to solve a wide range of tasks in the field of computer proteomics, including prediction of function, structure, and immune properties of proteins. A special section of the system allows the evaluation of quantitative and qualitative effects of mutations on the structural and functional properties of proteins. There are 19 different programs integrated into the system, including: PDBSite, a database of protein functional sites; PDBSiteScan, a program to predict functional sites in three-dimensional structures of proteins; and a Web-ProAnalyst program to quantitatively analysis the structure-activity relationships of proteins. The Protein Structure Discovery has a Web interface and is available for users via the Internet (http://www-bionet.sscc.ru/psd/). For example, the binding sites of zinc ion and ADP showed a high stability of the method to errors in the reconstruction of spatial structures of proteins in the recognition of functional sites in model structures.

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Authors and Affiliations

  1. Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr. Akad. Lavrent’eva 10, Novosibisk, 630090, Russia

    V. A. Ivanisenko, T. V. Ivanisenko & N. A. Kolchanov

  2. Sobolev Institute of Mathematics, Siberian Branch, Russian Academy of Sciences, pr. Akad. Koptyuga 4, Novosibisk, 630090, Russia

    P. S. Demenkov

Authors
  1. V. A. Ivanisenko
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  2. P. S. Demenkov
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  3. T. V. Ivanisenko
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  4. N. A. Kolchanov
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Correspondence to V. A. Ivanisenko.

Additional information

Original Russian Text © V.A. Ivanisenko, P.S. Demenkov, T.V. Ivanisenko, N.A. Kolchanov, 2011, published in Bioorganicheskaya Khimiya, 2011, Vol. 37, No. 1, pp. 22–35.

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Ivanisenko, V.A., Demenkov, P.S., Ivanisenko, T.V. et al. Protein structure discovery: A software package to computer proteomics tasks (Review). Russ J Bioorg Chem 37, 17–29 (2011). https://doi.org/10.1134/S1068162011010080

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  • DOI: https://doi.org/10.1134/S1068162011010080

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