Question about Protenix version upgrade and MSA support (ColabFold server) #12
Description
Thank you for releasing and maintaining PXDesign — it is a very impressive protein binder design framework.
While setting up and running the current codebase, I noticed that PXDesign is still using Protenix v0.5.0. At the same time, in the MSA generation workflow, ColabFold server–based MSA search does not appear to be supported yet, and the pipeline seems to rely on the older/local MSA setup.
This would be very helpful for users who want a more up-to-date MSA workflow.
Thank you very much for your time and for the great work on this project.