Dear Friends,
I have a question about judging a homology model. I
have three
homologous proteins A, B and C of which only A has 3D crystal structure
available. Their similarities/identities are given below.
Pair-wise alignment similarity/identity (%)
A and B 63/49
A and C 54/39
B and C 60/46
Assuming all the above data are right, which of the
following way would give the best model for C?
1. Building homology model of C with A as template.
2. Building homology model of B with A as template and then use B as
template to build C.
Suppose I used MODELLER for this work where an energy
minimization step is involved after threading the query sequence on the
template.
I need to know which model for C will be better and why?
Thanks for your answer…
Happy New Year to you all,
Raja
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