Is it possible to predict protein domains?

Ashok Aiyar aiyar at
Wed Sep 25 17:21:19 EST 1996

On 25 Sep 1996 15:39:18 GMT, Cornelius Krasel <krasel at> wrote:
>Hello folks,
>I wonder whether it might be possible to predict the domain structure
>of a protein without having to resort to sequence comparison. Are there
>preferred amino acids in the linkers between domains, or amino acids
>which are generally avoided?
>Something like this would definitely be useful for approaching several
>problems -- has anybody ever tried it?

I am not sure if the specific approach that you suggest has been
tried, but Patrick Argos had published an excellent paper in
JMB a few years ago on this subject.

The reference is:

J. Mol. Biol. 211: 943-958 (1990).  An investigation of oligopeptides
linking domains in protein tertiary structures and possible candidates
for general gene fusion.

I hope this helps you a little ....

Ashok Aiyar, Ph.D.
Department of Oncology            email: aiyar at
University of Wisconsin-Madison                  tel: (608) 262-6697

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