Hi all,
Apologies if this question has been previously posted on the list.
I modelled a sequence a while ago based on three templates using
Modeller- with pairwise sequence identities between target and templates:
45%, 38% and 34% (and positives or conserved substitutions in that order
as well).
When I overlaid the final model on top of the three templates
individually, I got a C alpha r.m.s.d. value of 3.0 Angs for the 45% ID
template, 0.6 Angs for the 38% one and 1.4 Angs for the 34% ID template.
How does Modeller deal with multiple templates? My initial thoughts would
be that the use of multiple templates would generally increase model
accuracy. Is there any reference for this? Also how do you account for the
highest sequence similarity template having the highest r.m.s.d of the
lot?
Does Modeller simply average out the templates from the multiple alignment
between the sequence and three templates in this case? Do other modelling
programs deal with this the same way?
Any comments would be greatly appreciated!
Best wishes,
Dinesh Soares
PhD Student
University of Edinburgh