I have two basic questions which I am desperate to get answers. Any body
there who can help me ?
-----------------------------------------------------------------------
1. In homology based modelling is it good to use single template or
multiple templates?
I have a cytochromep450 protein which shares maximum homology with another
protein of same class . But there were some missing residues in the template.
When used for modelling the region corresponding to this missing region had
bad environments in Verigy3D. I went on for loop modelling for this region.
But is this a good approach ?
I feel the alignment itself should take care of everything. I heard about
using multiple templates in such cases. How is this approach followed and
how good is it ?
--------------------------------------------------------------------------
2. I need to model some point mutations into this same protein sequence.
What is the best way of introducing mutations. Should the mutations be
introduced in the sequence and then modelled seperately, or should they be
introduced in the model of the wildtype ?
I want to do molecular dynamic simulations on Wildtype and Mutants to
compare and contrast the wildtype and mutant structures. What effect would
both these approaches have on the correctness of my results.
----------------------------------------------------------------------------
I'll be very grateful to you for your patience for all your suggessions
for my quieries.
Thanking you,
sridhar