Hi!
I need a denovo protein 3D model prediction tool for my own protein construct.
Nowadays you should really use one of the DeepLearning models for protein structure prediction, so AlphaFold2, ESMFold, OmegaFold, RosettaFold.
For AlphaFold2 there is a ready notebook to use from the collabfold project:
https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb
If your protein is short enough you can simply do this with the free computational power offered by google.
Sir I have tried to work on the AlphaFold2 but it is not working or running. My protein is is large.
Then you could try Metas ESMFold which is way faster. Also I found that you can easily predict protein sequences of up to ~2000AA relatively fast with the --cpu-only flag. As long as you have computation time available.
I don't know how available HPC is in Pakistan but from what I read on an wikipedia page you have ~10 Universities with supercomputers or something. So maybe you can get access ?
iTESSOR tool... It one of the most detailed and advanced 3D protein model prediction tool... I have used it in vaccine designing projects... It gives result in about 6 days...
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