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,