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
The bioinformatics discussion starts at 03:35.
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 AtlasWhat 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 GitHubThe group pageThe Folded Weekly newsletterA 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.