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[modeller_usage] Modelling Multiple Domains into One Multidomain Construct

Greetings Modeller community,

I am a complete noob to Modeller and I have read several papers which
point to Modeller for homology modeling.

My question is in essence "Can it be done using the Modeller?"

I have two structures for a multidomain protein (in different
conformations) from the different genus in the same family. The system I
am looking is also in the same family but different from the two I
mentioned above. I have the individual structures for each domain for my
system but I don't have the full length structure for my system. I would
like to model the individual domains onto the two full length structures
from the other genii. In addition, I also want to model the
substrate-bound forms of these domains from my system to the full length
structures from the other genii, but the full length structures in
either case does not contain the substrates. I have x-ray structures for
every one of them.

So can I use the substrate-bound or substrate-unbound x-ray structures
from my model to impose upon the full length structures? If I can, how
can I achieve it using Modeller?

Also if I read it correctly, Modeller optimizes the structure with MD
using the CHARMM potential function in vacuo. Is there a way to
incorporate the AMBER potential into Modeller and do optimization in
solvated form (e.g. in TIP3P shell)?

Finally, I was reading the Eramian et al. paper titled "How well the
accuracy of comparative protein structure models be predicted?". Is the
trained SVM available somewhere to predict the accuracy?

Thank you,

Cihan Aydin
UMass Graduate School of Biomedical Sciences
PhD Student @ Schiffer Lab

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