I’m new to both protein structure prediction and the use of AI-based tools like Alphafold2 or RoseTTAFold. And I have a few questions:
**1.** Is it possible to use structure prediction by AlphaFold2 to **validate** HMMER based domain sequence predictions?
If yes, what would be the steps? I have some idea, but not sure if it will work, and seek your input / advice?
**2.** For predicting structure of a protein domain sequence, should I feed the software
– the entire protein sequences, or
– just the domain sequence, or
– domain sequence + some bordering additional aa residues?
**3.** Currently for AlphaFold2, what are ready-to-use virtual machines that can be launched as an end-user,
rather than have me fumble with installation etc?
**4.** Is there any cloud-based server that provides not just approximate predictions, but results that i would obtain using the full install? For example, some of the google free-to-use python co-lab pages are not full implementations AFAIK, that use a shortcut for the computationally intensive MSA step, and so wouldn’t these predictions be not as accurate?
**5.** Would the prediction pipeline you suggest also be practical for high throughout prediction of structure to validate my domain predictions, where I can automate submission for ~1500 sequences (either full length protein or domain-only sequences)
Is it even possible to automate submission to some of the free-to-use Google’s Co-lab Py notebooks (from Martin Steinegger’s group)?