[modeller_usage] Homology Modeling of the Loop

[Alexander Predeus <>]

Hello all, 

I'm very much a beginner at modeling, and this question might be very trivial. I hope you still would hint me about the answer, for it would help me a lot. 

I have a large protein (say 1500 residues, let's call it protein A) and its homologue (protein B) of about the same size. Both proteins have published crystal structures.

Both proteins have a key structural element, loop L. The loop is poorly resolved in structure A, but well resolved in homologous structure B. 

Now, I can take just the L loop regions as separate PDB files from both A and B and do homology modeling of A based on B; this works really well. But I also would like the model to consider the surroundings (the rest of the structure) when evaluating the energies. 

Thus, I'd like to keep the REST of A's crystal structure intact, and only model loop L based on the structure of the same region in protein B. 

How can I achieve that? 

Thank you in advance!

- Alex Predeus
Michigan State University