Hi Tommi,
I suggest Rapper ( http://mordred.bioc.cam.ac.uk/~rapper/ ). If you scroll
down to the bottom of the page, you'll find references both for ab initio
an map-based modelling. If you don't want to experiment with Rapper - it
may take some time to learn how to use it - send me a private message for a
script that will rebuild a loop in an existing PDB file. I use this script
to rebuild loops in comparative models that were built without the template.
MODELLER ( http://salilab.org/modeller/modeller.html ) also can do ab
initio loop modelling.
Hope this helps,
Mensur
At 05:29 AM 11/1/2009, Tommi Kajander wrote:
>Dear all
>I was wondering if anyone knows a simple way to generate a missing
>loop (strech of amino acids)
>really in just some simple manner (no fancy minization necessary, of
>course some constraints probably dont
>hurt), just for visualization purposes of further simulations etc....
>
>thanks!
>tommi
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| Mensur Dlakic, PhD | Tel: (406) 994-6576 |
| Department of Microbiology | Fax: (406) 994-4926 |
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