Hmm, the CCD code option disappeared from the #AlphaFold3 server...

Outer product mean should go from MSA to pair representation.

Here is the performance of AlphaFold3-server vs. ColabFold-baseline on protein domains. AlphaFold3 is better for the majority of targets. I suspect that the weaker performance of AlphaFold3 in a couple of cases is due to using a reduced database for MSA construction.

Here is the plot for the protein complex predictions. AlphaFold3 server is an improvement over AlphaFold2 baseline represented by ColabFold. #CASP16