Aligned Sequences Heatmap

Very often we do not only want to know how certain proteins interact with their lipid environment but also compare their interaction profile with other proteins of the same class or family. The main challenge here comes from the increased data having to be visualized. A very effective way of doing it is by using heatmaps which map whatever underlying parameter (e.g. number of contacts or duration of contacts) to a color gradient.

An important thing to note here is that normalization of the data is done for each protein and each lipid individualy. This is important otherwise highly interacting lipids (like PIPs) or extreme outlier would skew the results and hide (potentially meaningful) differences.

The disadvantage of such a normalization is that you cannot compare result with one lipid to those of another. Additionally, the absolute magnitude of the parameters is lost (for instance, a high interaction of a residue with SM lipids might be high, but that is only compared to other residues' interactions with the same lipid). The advantage of this normalization are, however, numerous. We can easily compare results between residues within a GPCR and across all GPCRs. We can also, for example, easily see the difference in the interaction profile of residues that interact specifically with a lipid (say PIPs) and with a lipid that they do not interact specifically (say SM).