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From: Lucy Forrest lrf2103@columbia.edu Subject: modeling membrane protein loops

Hi,

In my experience (see ref below) the membrane does not affect modeling loops to any great extent.

However, when comparing different loop conformations energetically, if you treat the loop environment as vacuum then will get a much worse prediction than if you use solvation energy terms also.

Discrimination of native loop conformations in membrane proteins: Decoy library design and evaluation of effective energy scoring functions Proteins: Structure, Function, and Genetics Volume 52, Issue 4, Date: September 2003, Pages: 492-509 Lucy R. Forrest, Thomas B. Woolf

I can discuss this in more detail if anybody wishes, Lucy

Lucy Forrest Honig Lab Department of biochemistry Columbia University New York, NY 10032

>Date: 27 Aug 2003 11:37:52 -0400 >From: Andras Fiser afiser@aecom.yu.edu >Subject: Re: loop modeling > >Hello, > >It is right. Or as good as it gets, for two reasons, because Modeller >does not account for the environment explicitly anyway and loop modeling >will effect only the loop regions while keeping the rest of the >structure intact, irrespectively of how properly the rest was built. > >You will find a web interface to loop modeling in Modeller at >http://alto.compbio.ucsf.edu/modloop//modloop.html >that may help. > > >best wishes,Andras > >On Wed, 2003-08-27 at 02:32, Moshe Amitay wrote: > > >>Hi all, >>I whuld like your advice: >>I build a model of a membrane protein and I want now to do "loop modeling" >>to few extra cellular and intra-cellular loops. >> I wonder if this protocol of modeller is the right >>choice since the model doesn't contain the membrane and I actually ignore >>the influence of the polar heads. >> thank's >> Moshe Amity. >> >> >> >> >>

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