Protein Tertiary Structure Modeling

Nicolas Guex1, Torsten Schwede1, Manuel C. Peitsch1

1 Glaxo Wellcome Experimental Research, Geneva
Publication Name:  Current Protocols in Protein Science
Unit Number:  Unit 2.8
DOI:  10.1002/0471140864.ps0208s23
Online Posting Date:  May, 2001
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Abstract

Insights into the 3D‐structure of a protein have proven useful during experiment design. Experimentally elucidated structures are often not available, but comparative protein modeling provides a viable alternative in many cases. This unit presents comparative protein modeling and how to use the highly sophisticated but easy‐to‐use free software available on the Internet.

     
 
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Table of Contents

  • Glossary
  • Accessing SwissModel Programs and Documentation
  • ExPDB Database
  • Formatting a First Approach Modeling Request
  • Viewing SwissModel Results
  • Examples of SwissModel Requests
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
   Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403‐410.
   Bairoch, A. and Apweiler, R. 1999. The SwissProt protein sequence data bank and its supplement TrEMBL in 1999. Nucl. Acids Res. 27:49‐54.
   Chothia, C. and Lesk, A.M. 1986. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:823‐826
   Guex, N. and Peitsch, M.C. 1997. SwissModel and SwissPdbViewer: An environment for comparative protein modeling. Electrophoresis 18:2714‐2723.
   Guex, N., Diemand, A., and Peitsch, M.C. 1999. Protein modeling for all. Trends Biochem. Sci. 24:364‐367.
   Harrison, R.W., Chatterjee, D., and Weber, I.T. 1995. Analysis of six protein structures predicted by comparative modeling techniques. Proteins Struct. Func. Genet. 23:463‐471.
   Hooft, R.W.W., Vriend, G., Sander, C., and Abola, E.E. 1996. Errors in protein structures. Nature 381:272‐272.
   Peitsch, M.C. 1997. Large scale protein modeling and model repository. In Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology, Vol. 5 (T. Gaasterland, P. Karp, K. Karplus, C. Ouzonis, C. Sander, and A. Valencia, eds.) pp.234‐236. AAAI Press, Menlo Park, Calif.
   Sánchez, R. and Sali, A. 1998. Large‐scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl. Acad. Sci. U.S.A. 95:13597‐13602.
   Tilton, R.F., Dewan, J.C., and Petsko, G.A. 1992. Effects of temperature on protein structure and dynamics: X‐ray crystallographic studies of the protein ribonuclease‐A at nine different temperatures from 98 to 320 K. Biochemistry 31:2469‐2481.
   van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hünenberger, P.H., Krüger, P., Mark, A.E., Scott, W.R.P., and Tinoni, I.G. 1996. In Biomolecular Simulation: The GROMOS96 Manual and User Guide. Vdf Hochschulverlag ETH, Zurich (http://igc.ethz.ch/gromos/).
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