An update to #AlphaFold3 server. Now, you can add any ligand from the PDB using a CCD Code (up to 2024_10_28). Here is an MPro #SARS-CoV2 inhibitor from PDB 8u9h. The crystal structure is grey, and the #AF3 model is colored by pLDDT.

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