#67 AlphaFold and variant effect prediction with Amelie Stein

the bioinformatics chat

This is the third and final episode in the AlphaFold series, originally recorded on February 23, 2022, with Amelie Stein, now an associate professor at the University of Copenhagen.

In the episode, Amelie explains what 𝛥𝛥G is, how it informs us whether a particular protein mutation affects its stability, and how AlphaFold 2 helps in this analysis.

A note from Amelie:

Something that has happened in the meantime is the publication of methods that predict 𝛥𝛥G with ML methods, so much faster than Rosetta. One of them, RaSP, is from our group, while ddMut is from another subset of authors of the AF2 community assessment paper.

Other 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)
• A crime in the making: Russia’s atrocities — the podcast episode about the Olenivka prison massacre

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