Prediction of Protein-Protein Interactions Based on Molecular Interface Features and the Support Vector Machine

Protein-protein interactions play important roles in many biological progresses. 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 protein-binding sites and analyzed interface properties using 3D alpha shape. 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. In the experiment, our method shows best Matthews correlation coefficient of 0.204.