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Protein Modeling

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Handbook of Computational Chemistry

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Abstract

Proteins play a crucial role in biological processes, therefore, understanding their structure and function is very important. In this chapter we give an overview on computer models of proteins. First we treat both major experimental structure determination methods, X-ray diffraction and NMR spectroscopy. In subsequent sections computer modeling techniques as well as their application to the construction of explicit models are discussed. An overview on molecular mechanics and structure prediction is followed by an overview of molecular graphics methods of structure representation. Protein electrostatics and the concept of the solvent-accessible surface are treated in detail. We devote a special section to dynamics, where time scales, structures, and interactions are discussed. Protein interactions are especially important, so protein hydration, ligand binding, and protein–protein interactions receive special attention. Finally, computer modeling of enzyme mechanisms is discussed. We try to demonstrate that protein representation by computers arrived to a very high degree of sophistication and reliability; therefore, even lots of experimental studies make use of such models. A list with 80 up-to-date bibliographic references helps the reader to get informed on further details.

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Acknowledgments

We are indebted to our colleagues, Dr. Z. Gáspári, Dr. V. Harmat, and Ms. P. Rovó for important remarks on the manuscript and providing most of the figures.

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Authors and Affiliations

  1. Laboratory of Structural Chemistry and Biology and Protein ModellingGroup HAS-ELTE, Institute of Chemistry, Eötvös Loránd University, P.O.Box 32, 1117, Budapest, Hungary

    G. Náray-Szabó, A. Perczel & A. Láng

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  1. G. Náray-Szabó
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  2. A. Perczel
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  3. A. Láng
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Editors and Affiliations

  1. Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, 39217, USA

    Jerzy Leszczynski

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Náray-Szabó, G., Perczel, A., Láng, A. (2012). Protein Modeling. In: Leszczynski, J. (eds) Handbook of Computational Chemistry. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-0711-5_30

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