AlphaFolding the Protein Universe

July 22, 2021

Hot on the tail of our inclusion of the Baker group’s trRosetta structural models we are excited to announce the inclusion of models from AlphaFold 2.0 generated by DeepMind and stored in the AlphaFold Database (AlphaFold DB). AlphaFold 2.0’s performance in the CASP14 competition was spectacular, producing near experimental quality structure models.

The new AlphaFold models have been constructed for over 375,000 proteins from 22 model organisms and the very large majority of the models are full length proteins. This is in contrast to the trRosetta models, which were built from the domain region predicted by Pfam. Having full length protein models is very exciting for us because it will allow us to more easily check whether we need to extend or change the Pfam domain boundaries.  We will also be able to look for missing domains in the protein structures. AlphaFold models also help to fill in gaps when only a part of a longer family has been structurally characterised.

When looking at the AlphaFold models it is important to look at the quality scores of the model overall. Sometimes a good quality structural model cannot be created, but in these cases it is usually obvious from the quality scores shown as orange regions of the model.  Disordered regions of proteins are usually of low confidence.

We think that there are many thousands of Pfam families that could be improved using the AlphaFold and trRosetta models. Feel free to tell us where we could improve them. We are really enjoying mining this treasure trove of data and we hope you find some (not so) hidden gems. 

The Pfam team

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