Prediction of protein-protein interactions using alpha shape modeling

Abstract

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. © 2011 American Institute of Physics.