How to precompute Protenix-compatible MSAs locally

[mestia]

According to the documentation, Protenix has the capability to utilize ColabFold results for preparing Protenix-compatible MSAs. However, if I understand this correctly, it appears that the MSA step must be executed twice: first with ColabFold, and then with Protenix. Both steps require approximately the same time and seem to scan the same databases. Is there a direct method to generate Protenix-compatible MSAs locally without doubling the overall processing time?

[zhangyuxuann]

@mestia If you generate Protenix-compatible MSAs locally using colabfold, it will not search MSAs again by ProteniX Pipeline. #39