Hello all, <br><br>I&#39;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. <br><br>I have a large protein (say 1500 residues, let&#39;s call it protein A) and its homologue (protein B) of about the same size. Both proteins have published crystal structures.<br>
<br>Both proteins have a key structural element, loop L. The loop is poorly resolved in structure A, but well resolved in homologous structure B. <br><br>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. <br>
<br>Thus, I&#39;d like to keep the REST of A&#39;s crystal structure intact, and only model loop L based on the structure of the same region in protein B. <br><br>How can I achieve that? <br><br>Thank you in advance!<br><br>
- Alex Predeus<br>Michigan State University <br>