Welcome to the “one stop shop” for yeast protein topology predictions. To help you figure out what your protein may look like – we have pooled together the predictions of 9 highly utilized prediction algorithms in a graphical output.

The function, substrate accessibility, physical interactions and regulation of proteins are all highly dependent on their location in the cell and whether they span a membrane or not and if so in what topology. Assignment of a protein as a membrane spanning one relies primarily on prediction algorithms for transmembrane domains (TMDs) and topology assignment. Several different algorithms exist in the field (click here to see the algorithms we used for this website). The prediction of these algorithms can be highly variable in their topology and TMDs assignments. And so, most predictions based on a single algorithm may be incorrect whereas exploration of several options is time-consuming and elaborate.

We did not program any of these prediction algorithms but find that it is very useful to look at multiple topology predictions in parallel when trying to assess which is the right one… Hence to help people interested in specific proteins we have here compiled the predictions from nine publicly available TMD and topology algorithms (click here to see which ones we picked) on all Saccharomyces cerevisiae proteins. We have also added specific predictions for the presence of signal peptides or Mitochondrial Targeting Sequences (MTS). We also added some experimental data on N’ orientation and the presence of an MTS. For more info about programs and data

Most importantly, we have built a graphical output that we believe allows the user to inspect all TMD and topology predictions for any yeast protein simultaneously and easily get a sense of which might be right. You are welcome to search for any specific protein or a list of proteins or download all of the graphical data or source data.