Protein‐protein interactions play important roles in a lot of biological progress. Previous studies about protein‐protein interactions were mainly based on sequence analysis. As more 3D structural information can be obtained from protein‐protein complexes, structural analysis becomes feasible and useful. In this study, we used structural alignment to predict the protein‐binding site and apply 3D alpha shape modeling to analyze the interface characteristics. We have developed a method for protein‐protein interaction prediction. The result indicates good performance of our method in discriminating protein‐binding structures from non‐protein binding structures. Our method outperforms the previous methods based on the Matthews correlation coefficient.

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