Hi,

I am trying to model circular permutation in my protein which is a beta barrel and I modeled it the following way--

AAAA-----BBB
--------CCC-------

A and B comprise the two halves of beta barrel and ---- refers to a cut in the loop region of beta barrel where the other domain has to be attached ...

I generated some 20 models but none of them was satisfactory as the beta-barrel gets distorted in each of those models..

Can any body tell how can I achieve good models for modeling circular permutation ???




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Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
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