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)?
Thanks in advance.