Subject: CCL:Folding

From: [email-masked] (Klaus J.W.May)
Date: Wed, 25 Oct 1995 23:03:13 +0200

>Date: Wed, 25 Oct 1995 22:43:33 +0200
>From:[email-masked] (Klaus J.W.May)
>Subject:Re: CCL:Folding
>
>>Dear Netters,
>>
>>here is my question: is there a program that allows one to fold a protein
>>of which only the sequence is known, on the basis of the folding of
>>a similar one? How high should be the omology of the two?
>>
>>My actual problem is: I have the sequence of a protein, but no x-ray nor
>>NMR structure is available, and I would like to do dynamics and/or 
>>modeling on that.
>>As usual, any suggestion is welcome. Thank you.
>>Cheers, 
>>Antonio
>
>Owtch,
>
>dear Antonio,
>
>a complicated problem! If one could give you the final answer, he/she is
>probably a good candidate for the Nobel price.
>You can approach the problem gradually. Are there other structures (Xray)
>known of proteins with functional homology? Then you could go with Biosym's
>Homology Program or use Eisenberg's approach. 
Or look at  George Rose's recent Papers in" Proteins" 
Are there clear secondary structural domains ( there are many programs
around, which do that analysis - some better, some worse - it's mainly a
function of the scoring matrix)? 
>You can use those motifs to proceed gradually into larger arrangements -
>always with a close eye on known structures ( have a look at Articles from
>Jane and Dave Richardson). Probably you'll start with Polyalanine and take
>care of the sidechaines later. Lucky one, when you have defined disulfides in
>your structure - this alrady helps a lot.
>
>An excellent program to help you to interacively model motifs of secondary
>structure, do chainpacking studies down to the energeticly meaningful
>manipulation of single atoms is SCULPT from Interactive Simulations. You can
>download the program ( in a timebombed demoversion) from
>http://www.intsim.com/~isigen. It's for free. There are also some meaningful
>demostructures from actual scientific research work which can give you some
>ideas of how to possibly approach your problem.
>
>This Demoversion runs on an SGI. There is now a first Versiobn for the
>Powermacintosh available - with astounding speed!  A PC version is coming
>later this year.
>
>Hope this helps at least a little bit in your complicated problem.
>
>Almost forgot:  There is a simple solution : just crystallize it and do the
>structure   :-)
>
>Cheers
>Klaus
>

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