A method for extracting pathways from Scansite-predicted protein-protein interactions

Protein interaction is an important mechanism for cellular functionality. Predicting protein interactions is available in many cases as computational methods in publicly available resources (for example Scansite). These predictions can be further combined with other information sources to generate hypothetical pathways. However, when using computational methods for building pathways, the process may become time consuming, as it requires multiple iterations and consolidating data from different sources. We have tested whether it is possible to generate graphs of protein-protein interaction by using only domain-motif interaction data and the degree to which it is possible to automate this process by developing a program that is able to aggregate, under user guidance, query results from different information sources. The data sources used are Scansite and SwissProt. Visualisation of the graphs is done with an external program freely available for academic purposes, Osprey. The graphs obtained by running the software show that although it is possible to combine publicly available data and theoretical protein-protein interaction predictions from Scansite, further efforts are needed to increase the biological plausibility of these collections of data. It is possible, however, to reduce the dimensionality of the obtained graphs by focusing the searches on a certain tissue of interest