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 The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/