The genome-wide identification of pairs of interacting proteins is an important step in the elucidation of cell regulatory mechanisms. To date, structural information has had only limited impact on genome-scale efforts to predict protein-protein interactions (PPIs). A new algorithm, PrePPI, will be introduced that combines structural information with non-structural clues and that is comparable in accuracy to high-throughput experiments. The surprising effectiveness of three-dimensional structural information can be attributed to the use of homology models and the exploitation of both close and remote geometric relationships between proteins. More generally, the “structural BLAST” approach encapsulated in PrePPI significantly expands the range of application of protein structure in the annotation of protein function.

This research has been supported by NIH GM030518, GM094597 and CA121852.

References

Zhang, Q.C., Petrey, D., Deng, L., Qiang, L., Shi, Y., Thu, C.A., Bisikirska, B., Lefebvre, C., Accili, D., Hunter, T., Maniatis, T., Califano, A. and Honig, B. (2012) Structure-based Prediction of Protein-protein Interactions on a Genome-wide Scale. Nature 490, 556 - 560.

Zhang, Q.C., Petrey, D., Garzon, J.I., Deng, L. and Honig, B. (2013) PrePPI: A Structure-Informed Database of Protein-Protein Interactions. Nucl. Acid Res. 41, D828-833.