Where do the data come from?

Methods for molecular interaction identification

There are roughly two fundamental ways to gaining information about molecular interactions:

• computational
• experimental

In this course we will concentrate on experimental methods, but there is an increasing variety of computational methods that can predict protein-protein interactions. Because only a small proportion of all the molecular interactions in an organism are currently covered by experimental data, these methods provide a meaningful resource that can help use to analyse under-represented regions of the interactome. You can find out more about the different methods used to predict protein-protein interactions in a comprehensive Wikipedia entry entitled protein-protein interaction prediction.

A wide variety of experimental methods can be used to detect protein-protein interactions. It is important to realise that there is no perfect approach. Each method has its limitations and is to an extent potentially artifactual. Therefore, it is advisable to check interactions using more than one approach: interactions detected by more than one method are more likely to be “real”.^4,5,6

Next, we will have a look at some ways to experimentally identify protein-protein interactions.