Accurate Prediction of Protein Complex Stoichiometry by Integrating AlphaFold3 and Template Information

Protein structure prediction methods require stoichiometry information (i.e., subunit counts) to predict the quaternary structure of protein complexes. However, this information is often unavailable, making stoichiometry prediction crucial for complexes with unknown stoichiometry. Despite its importance, few computational methods address this challenge. In this study, we present an approach that integrates AlphaFold3 structure predictions with homologous template data to predict stoichiometry. The method generates candidate stoichiometries, builds structural models for them using AlphaFold3, ranks them based on AlphaFold3 scores, and further refine predictions with template-based information when available. In the 16th community-wide Critical Assessment of Techniques for Protein Structure Prediction (CASP16), our method achieved 71.4% top-1 accuracy and 92.9% top-3 accuracy, outperforming other predictors in terms of the overall performance. This demonstrates the complementary strengths of AlphaFold3- and template-based predictions and highlights its applicability for uncharacterized protein complexes lacking stoichiometry data.