Erice2010:Workshop9

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MODELLER/IMP workshop

This is the detailed information for workshop #9, MODELLER and IMP, led by Ben Webb, UCSF.

Aim

MODELLER and IMP are packages that generate structural models of proteins and their assemblies that are consistent with all known physical, statistical and experimental information, by application of the method of satisfaction of spatial restraints.

  • MODELLER generates homology or comparative models of single proteins for which the sequence (but not the structure) is known, by using the known structures of other proteins that have similar sequences as templates.
  • IMP extends the method used in MODELLER to the determination of the structures of protein assemblies, by combining disparate sources of experimental information, such as cryo-EM, SAXS, and proteomics.

This workshop will demonstrate the use of MODELLER to generate and validate comparative models, show how additional experimental data can be added to improve the model quality, and introduce the new IMP package.

Suitability

This workshop is suitable for complete novices. Expert users are recommended to contact Ben (ben at salilab dot org) before the workshop. If there are advanced areas that people are interested in covering, we can meet informally during the Erice workshop.

Materials

Suggested reading before the workshop:

  • MODELLER
    • Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.
    • Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000.
  • IMP
    • Determining the architectures of macromolecular assemblies. Nature 450, 683-694, 2007.
    • The molecular architecture of the nuclear pore complex. Nature 450, 695-701, 2007.

See also our website.

The workshop will be "watch me" style, but if you wish to follow along yourself (or want to rerun the examples after the workshop) you will need to install Modeller and download the example files, in tar.gz format or zip format.

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