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