http://wiki.docking.org/index.php?action=history&feed=atom&title=Erice2010%3AWorkshop9 2026-05-25T07:17:31Z Revision history for this page on the wiki MediaWiki 1.39.1 http://wiki.docking.org/index.php?title=Erice2010:Workshop9&diff=2698&oldid=prev 2012-10-08T20:17:53Z

<p>4 revisions</p> <p><b>New page</b></p><div>= MODELLER/IMP workshop =<br /> <br /> This is the detailed information for workshop #9, MODELLER and IMP, led by Ben Webb, UCSF.<br /> <br /> {{TOCright}}<br /> <br /> = Aim = <br /> 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.<br /> <br /> * 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.<br /> <br /> * 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.<br /> <br /> 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.<br /> <br /> = Suitability = <br /> 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.<br /> <br /> = Materials = <br /> Suggested reading before the workshop:<br /> <br /> * MODELLER<br /> ** Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.<br /> ** Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000.<br /> * IMP<br /> ** Determining the architectures of macromolecular assemblies. Nature 450, 683-694, 2007.<br /> ** The molecular architecture of the nuclear pore complex. Nature 450, 695-701, 2007.<br /> <br /> See also [http://salilab.org our website].<br /> <br /> The workshop will be &quot;watch me&quot; style, but if you wish to follow along yourself (or want to rerun the examples after the workshop) you will need to [http://salilab.org/modeller/download_installation.html install Modeller] and download the example files, in [http://salilab.org/modeller/erice.tar.gz tar.gz format] or [http://salilab.org/modeller/erice.zip zip format].<br /> <br /> [[Portal:Erice2010 | return to main workshop page]]<br /> <br /> [[Category:Erice2010]]</div>

Therese http://wiki.docking.org/index.php?title=Erice2010:Workshop9&diff=2694&oldid=prev 2010-04-01T05:46:04Z

<p>update to 2010 (still looks like a stub)</p> <p><b>New page</b></p><div>This is the detailed information for workshop #9, MODELLER, by Webb, Erice 2010. <br /> {{TOCright}}<br /> = Aim = <br /> The aim of this workshop is <br /> <br /> = Suitability = <br /> This workshop is suitable for complete novices. If you are an expert, suggest you contact Eswar for conversation during the meeting.<br /> <br /> = Materials = <br /> papers to read before the workshop <br /> * one<br /> * two <br /> * three<br /> websites to review before the workshop <br /> * [http://salilab.org ]<br /> <br /> = Protocol = <br /> Here are the step by step instructions for doing the workshop<br /> <br /> * 1. go to ...<br /> * 2. do this ...<br /> * 3. do that ....<br /> <br /> = Extras = <br /> Here are the &quot;bonus projects&quot; you may work on if you finish the workshop early. <br /> <br /> * 1. <br /> <br /> <br /> [[Portal:Erice2010 | return to main workshop page]]<br /> <br /> [[Category:Erice2010]]</div>

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