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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