the bioinformatics chat

This is the second episode in the AlphaFold series, originally recorded on February 14, 2022, with Janani Durairaj, a postdoctoral researcher at the University of Basel.

Janani talks about how she used shape-mers and topic modelling to discover classes of proteins assembled by AlphaFold 2 that were absent from the Protein Data Bank (PDB).

The bioinformatics discussion starts at 03:35.

Links:

• A structural biology community assessment of AlphaFold2 applications (Mehmet Akdel, Douglas E. V. Pires, Eduard Porta Pardo, Jürgen Jänes, Arthur O. Zalevsky, Bálint Mészáros, Patrick Bryant, Lydia L. Good, Roman A. Laskowski, Gabriele Pozzati, Aditi Shenoy, Wensi Zhu, Petras Kundrotas, Victoria Ruiz Serra, Carlos H. M. Rodrigues, Alistair S. Dunham, David Burke, Neera Borkakoti, Sameer Velankar, Adam Frost, Jérôme Basquin, Kresten Lindorff-Larsen, Alex Bateman, Andrey V. Kajava, Alfonso Valencia, Sergey Ovchinnikov, Janani Durairaj, David B. Ascher, Janet M. Thornton, Norman E. Davey, Amelie Stein, Arne Elofsson, Tristan I. Croll & Pedro Beltrao)
• The Protein Universe Atlas
• What is hidden in the darkness? Deep-learning assisted large-scale protein family curation uncovers novel protein families and folds (Janani Durairaj, Andrew M. Waterhouse, Toomas Mets, Tetiana Brodiazhenko, Minhal Abdullah, Gabriel Studer, Mehmet Akdel, Antonina Andreeva, Alex Bateman, Tanel Tenson, Vasili Hauryliuk, Torsten Schwede, Joana Pereira)
• Geometricus: Protein Structures as Shape-mers derived from Moment Invariants on GitHub
• The group page
• The Folded Weekly newsletter
• A New York Times article about the Kramatorsk missile strike. The Instagram video, part of which you can hear at the beginning of the episode, appears to have been deleted.

If you enjoyed this episode, please consider supporting the podcast on Patreon.