Structure comparison of heme-binding sites in heme protein predicted by AlphaFold3 and AlphaFold2

Abstract

AlphaFold3 can predict protein–ligand complex structures. In this study, we examined the accuracy of prediction of heme–protein interactions by AlphaFold3. AlphaFold3 succeeded in predicting heme–protein interactions for most heme proteins except for those without homologous proteins in the Protein Data Bank. Our comparison of predictions by AlphaFold3 and AlphaFold2 suggests that heme–protein structures can be predicted from amino acid sequences of proteins alone using AlphaFold2.