Predicting the 3D structure of a protein

Question

[nbnbs727]

I would like to predict the 3Dstructure of a membrane protein. I cannot use homology modeling because the similarity with the template is less than 30%. In this case, which method I have to use for predicting the 3D structure? I also need to predict the ligands for the modeled protein. Your suggestions would be appreciated!

[natasha.sernova]

According to this page: https://blanco.biomol.uci.edu/mpex/

it may be used.

Answer 1

[dasdevashishdas]

You have two option:

1. Consider multiple template and go for homology modelling
2. Do Protein threading prediction (http://zhanglab.ccmb.med.umich.edu/I-TASSER/)

Answer 2

[natasha.sernova]

See this article. It looks useful.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108304/

see table1 to find useful urls.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108304/table/T1/

See membrane protein explorer link below:

http://blanco.biomol.uci.edu/mpex/

[nmt980]

Hii natasha.sernova....I have an query regarding mpex...that whether it can be used for hydropathy analysis as well?