Webinar: New Era of Structure Abundance - Insights into Protein Function

Tue 10 October 2023, 17:00

This webinar is by the ELIXIR 3D-BioInfo Community, chaired by Dr. Mihaly Varadi

Dr. Joana Pereira, 

Biozentrum, University of Basel 

(joana.pereira [at] unibas.ch)


"Uncovering new families and folds in the natural protein universe"

“Thanks to the deep learning revolution in bioinformatics, we are now entering a new era in protein structural biology. There are hundreds of millions of predicted protein structures made available through the AlphaFold database, which cover nearly all proteins that are known. This include not only those already covered by the PDB but also those that are challenging to computationally annotate for function or putative biological role. We examined the extent to which the AlphaFold database has structurally illuminated this “dark matter” of the natural protein universe at high predicted accuracy and described the protein diversity that they cover as an annotated interactive sequence similarity network. By searching for novelties from sequence, structure, and annotation perspectives, we uncovered new novel folds, found a new superfamily of translation-targeting toxin-antitoxin systems, and added multiple protein families to Pfam. Our work underscores the value of large-scale efforts in identifying, annotating, and prioritising novel protein families. By leveraging this revolution, we can now shed light into uncharted areas of the protein universe at an unprecedented scale.”


Dr. Manjeet Kumar,

European Molecular Biology Laboratory

(manjeet.kumar [at] embl.de)

“Eukaryotic Linear Motif (ELM) resource - updates, annotation challenges, and impact of AlphaFold2 and AlphaFold DB on motif-mediated PPIs”
The talk will cover recent updates on the Eukaryotic Linear Motif (ELM) resource, a hub for exploring the Short Linear Motifs (SLiMs). Other than sharing the latest biological insights from the database, I will also discuss the challenges encountered during the annotation process, including distinguishing functionally relevant motifs and the missing cellular context. The last part of the talk will focus on the impact of AlphaFold2 (AF2)/AlphaFold predicted models (AFDB) in advancing our understanding of motif-mediated protein-protein interactions (PPIs) and their functional relevance.


This webinar will be chaired by 

Dr. Mihaly Varadi,

European Bioinformatics Institute

(mvaradi [at] ebi.ac.uk)

All previous webinars from the 3d-BioInfo Community are available here




Programme: Dr. Sameer Velankar (European Bioinformatics Institute)
Event administration: Dr. R. Gonzalo Parra (gonzalo.parra@bsc.es)

See also: 3D-BioInfo Community