I am working on IL 4R Alpha where in I have to build a model for wild type and mutant. The problem which I am facing is that template available for this protein is of 202-218 AA length wrt Human in PDB while my protein is of 825 AA. And when I am looking for closely associated protein structure using ORION web server the length is equal or greater than 825 AA but their percent identity is significantly low. Any lead in this problem is much appreciated.
Run AlphaFold. https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb
Hi, apart from Woonghee Lee 's answer regarding Afold, you can use some other tools as well such as I-Tasser from Zhang Lab.
For homology modeling, how low do you have the similarity?
You can follow guides regarding homology modeling from this article:
Article Ten quick tips for homology modeling of high-resolution prot...
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