Modelling complexes
Dear all,
I'm new with modeller, I have used it to do simple models.. However I'm now trying to model a tri-metric complex where the active site of the complex is includes all three subunits. How do i go about this?
kind regards
Chido
-------------------------------------------------- Dr Chido M'pamhanga Biological Chemistry and Molecular Microbiology School of Life Sciences University of Dundee Dow St. Dundee, DD1 5EH U.K. +44 (0)1382 386229(phone) +44 (0)1382 386373 (fax) http://www.brenkgroup.dundee.ac.uk
Chido Mpamhanga wrote: > I'm new with modeller, I have used it to do simple models.. However I'm > now trying to model a tri-metric complex where the active site of the > complex is includes all three subunits. How do i go about this?
Building multi-chain models is straightforward, particularly if you have a multimeric template - just add chain breaks ('/') to your alignment where needed. See the example in the manual: http://salilab.org/modeller/9v3/manual/node28.html
If you have ligands which interact with two or more chains, Modeller should handle them correctly, as the constraints are distance-based, not sequence-based.
Ben Webb, Modeller Caretaker
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Chido Mpamhanga
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Modeller Caretaker