Help for building Pipeline for Modeller

Question

[Muhammad Saad]

Good wishes, everyone. I'm Saad, a beginner in Bioinformatics. I uses modeller multiple times but its manuality often seems outdated to me. Did anyone try to automate the process for finding missing residues by building the pipeline? A pipeline that should be given input.pdb and input.fasta to generate the .seq file and then should use the emboss for the allignment and format it according to modeller acceptable format automatically. Further, it should use that .ali file and predict the structure. Let me know if anyone tried or if not. Help me in building the one for myself. Regards...

[Muhammad Saad]

This one is my first post here. Looking forward to learn amazing things.

Answer 1

[Mensur Dlakic]

There are more than 200 million protein models in the AlphaFold database:

https://alphafold.ebi.ac.uk/

Chances are high that either a model of your protein of interest is already there, or something homologous to it.

I used Modeller a lot back in the day, but it is a difficult program to master. Not something that anyone can explain in a single internet post. For that time investment to be worth it, Modeller would have to produce models that are better than other available options. It won't. Like I said, either a model is already made for your protein, or you can make one on your own by using the following links:

• https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb
• https://alphafoldserver.com