Dear Alex, It is pretty simple. Simplest way is to make the alignment file with your loop region well aligned to corresponding chunk in structure B and for other residues, put gap in your alignment file for structure A, corresponding to respective additional residues in structure B. You may use the PRALINE alignment to do it and pipeline that to MODELLER.

There is one more way too to consider the environmental effects on structural topology of A as per the structure B. Ashish

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

----- Original Message ----- From: "modeller usage-request" modeller_usage-request@salilab.org To: "modeller usage" modeller_usage@salilab.org Sent: Tuesday, November 1, 2011 9:31:40 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 134

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Today's Topics:

1. Homology Modeling of the Loop (Alexander Predeus) 2. Re: modeller_usage Digest, Vol 10, Issue 132 (Ashish Runthala)

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Message: 1 Date: Mon, 31 Oct 2011 15:02:46 -0400 From: Alexander Predeus predeus@gmail.com Subject: [modeller_usage] Homology Modeling of the Loop To: modeller_usage@salilab.org Message-ID: CADvsxO=iHEGXCyUW=DfC7GrRumcYcfgUYxmp5gnPjGC5Cff73w@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"

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