Should you use multiple pdb files of the same sequence when available for multiple template homology modeling?
Hi,
Among the proteins exhibiting homology to my sequence of interest is a protein that has been cristallized with three different ligands by the same team. I was wondering if, when faced with this kind of situation, including all three structures in the homology modeling would introduce a bias. Do you think I should pick one of the structures (based on compare.py) or include all of them in my multiple template modeling?
meginir,
On 5/5/14, 1:38 AM, meginir urestal wrote: > Among the proteins exhibiting homology to my sequence of interest is a > protein that has been cristallized with three different ligands by the > same team. I was wondering if, when faced with this kind of situation, > including all three structures in the homology modeling would introduce > a bias. Do you think I should pick one of the structures (based on > compare.py) or include all of them in my multiple template modeling?
In principle including all three of them (assuming they're all of the same fold) would allow Modeller to use the most information.
Ben Webb, Modeller Caretaker
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meginir urestal -
Modeller Caretaker