Hi
I want to model a receptor protein (Vasopressin 1b) with uniprot id P47901. The third IC loop needs to be handled with more precautions due its long length. I can assure you that the credit for your help with be definitely given.
Thank you
Hi Rahul,
I-Tasser can help you to model the receptor and Molprobity to validate the constructed model.
https://zhanglab.ccmb.med.umich.edu/I-TASSER/
http://molprobity.biochem.duke.edu/
Hi Mr Bello
I have tried all these servers but the difficulty is with the loop region. They come in contact with helix due to its length.
Kindly help solve this issue
Hi Mr Dalal
Thanks for your valuable reply. I have attached the best modeled structure I could come up with after using various servers and HM. (Non-simulated structure). Please kindly have a look at the IC3 and terminals. They are too long and yet in unacceptable position. Can you add some ideas to lit me up on this problem.
At the same time, rather using the whole IC3, i prefer replacing the loop with shorter one as my work doesn't concentrate on loop regions. How about clipping the loop to small version?
Dear Dalal,
The structure added here is modeled using I-Tasser. I have no strong background on Homology modeling or any other kind of modeling. With little knowledge I could come up with the above structure. your statement " your protein has alignment from residue 38 to 345 " refers to what actually?
I tried modeler for the uniprot sequence and couldn't come with any kind of solutions. The availability of template was almost nil to the limited practice I have on modeler.
Hi
Sorry Mr Dalal, I have tried all these servers and i-Tasser give the better of all. Still I want to refine the loop regions and terminals.
Modloop can accept only 14 residues from a loop, that is not the case in our problem. Mr dalal thank you for your time. Kindly share if you have any more details
You can do protein homology modelling using Modeller. Modeller is most commonly used software for protein homology modelling. ModellerJ is an easy to use interface for Modeller. https://www.youtube.com/channel/UCQcgP49rantOASQ_zP2QPXQ/featured
Yogesh Gaikwad Thank you so much Sir. I tried to my best. But couldn't solve the structure.
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