Subject: CCL: Protein Domain Prediction

From: "Shoba Ranganathan" <[email-masked]>
Date: Wed, 7 Jun 1995 15:36:26 +0000

Hi,

Is there any method/program that can successfully identify domain 
boundaries from the amino acid sequence of a protein?  This will be a 
first step towards inverted protein structure prediction, I believe.

Shoba
===========================================================
Dr. Shoba RANGANATHAN                   Tel: +616-279-8301  
Div. of Biochemistry & Mol. Biology     Fax: +616-249-0415             
JCSMR, Australian National University                              
Canberra ACT 2002                       
Australia.              email:[email-masked]
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From: [email-masked] (C.S.RAMAN)
Date: Wed, 7 Jun 1995 11:32:34 -0500 (CDT)

> first step towards inverted protein structure prediction, I believe.

You might want to take a look at the following paper from Kahn's group
in Toulouse.  It provides a method for identifying domains in proteins

Sonnhammer EL; Kahn D.
     Modular arrangement of proteins as inferred from analysis of homology.
   Protein Science, 1994 Mar, 3(3):482-92.

In addition, you can use the database used in this study to evaluate the
domain structure of your protein, by sending an email to:

[email-masked]

To get a help file, send the message "help" in the body of your message.

Also, see the recent paper by Sowdhamini and Blundell in Protein Science
[1995] 4, 506-520 "An automatic method involving cluster analysis of
secondary structures for the identification of domains in proteins".

Regards
-raman
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