Protein Modeling

  • G. Náray-Szabó
  • A. Perczel
  • A. Láng
  • D. K. Menyhárd
Living reference work entry


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 of molecular motions, structures, and interactions are discussed. Protein in relation to its surroundings is especially important, so protein hydration, ligand binding, and protein-protein interactions receive special attention. The case study of podocin provides an example for the successful application of molecular dynamics to a complex issue. At last, computer modeling of enzyme mechanisms is discussed. It is demonstrated 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 a large number of up-to-date bibliographic references helps the reader to get informed on further details.


Nuclear Magnetic Resonance Nuclear Magnetic Resonance Spectroscopy Solvent Accessible Surface Area Nuclear Overhauser Effect Residual Dipolar Coupling 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



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


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© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • G. Náray-Szabó
    • 1
  • A. Perczel
    • 1
  • A. Láng
    • 1
  • D. K. Menyhárd
    • 1
  1. 1.Laboratory of Structural Chemistry and Biology, Institute of ChemistryEötvös Loránd University and MTA-ELTE Protein Modelling Research GroupBudapestHungary

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