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I have: 1. A PDB dimer protein structure template of a real solved protein. 2. An unsolved, but highly homologous dimer protein (>90% sequence identity.)

How can I use MODELLER to make a theoretical model of my dimer of unknown structure, using the homologous dimer template?

I know I need a PIR alignment file, probably with a 1:1 sequence-structure alignment. However, I do not know how to make this file.

Please advise?

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