------ Forwarded Message
From: Lucy Forrest <>
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 <>
>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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