Ankh-score produces better sequence alignments than AlphaFold3

Protein sequence alignment is one of the most fundamental procedures in bioinformatics. Due to its many downstream applications, improvements to this procedure are of great importance. We consider two revolutionary concepts that emerged recently as candidates for improving the state-of-the-art alignment methods: AlphaFold and protein embeddings. Alignment improvements can come from structural alignment of AlphaFold-predicted structures or scoring based on similarity of protein embedding vectors, resp. Thorough comparison on many domains from BAliBASE and CDD demonstrates that the Ankh-score method produces much better sequence alignments than structural alignments using US-align of AlphaFold3-predicted structures. Both are better than the traditional method using BLOSUM matrices. This suggests that Ankh embedding vectors may possess certain information that is not available in the AlphaFold3-predicted structures.