This is an archived file from the Spring 2022 version of the course.
See the current course website for a more recent version.

Class 24: Protein Folding and AlphaFold

Schedule

Project Update: due tomorrow, Tuesday, 19 April, 4:59pm.

Submission Form

Slides

Slides: class24.pdf

  • Ken A. Dill, S. Banu Ozkan, M. Scott Shell, and Thomas R. Weikl. The Protein Folding Problem. Annual Review of Biophysics, 2008.

  • Bonnie Berger and Tom Leighton. Protein Folding in the Hydrophobic-Hydrophilic Model is NP-Complete. RECOMB 1998.

  • Scott Aaronson, NP-complete Problems and Physical Reality.

  • Andrew W. Senior, Richard Evans, John Jumper, James Kirkpatrick, Laurent Sifre, Tim Green, Chongli Qin, Augustin Žídek, Alexander W. R. Nelson, Alex Bridgland, Hugo Penedones, Stig Petersen, Karen Simonyan, Steve Crossan, Pushmeet Kohli, David T. Jones, David Silver, Koray Kavukcuoglu, and Demis Hassabis. Improved protein structure prediction using potentials from deep learning. January 2020.

  • John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko, Alex Bridgland, Clemens Meyer, Simon A. A. Kohl, Andrew J. Ballard, Andrew Cowie, Bernardino Romera-Paredes, Stanislav Nikolov, Rishub Jain, Jonas Adler, Trevor Back, Stig Petersen, David Reiman, Ellen Clancy, Michal Zielinski, Martin Steinegger, Michalina Pacholska, Tamas Berghammer, Sebastian Bodenstein, David Silver, Oriol Vinyals, Andrew W. Senior, Koray Kavukcuoglu, Pushmeet Kohli, and Demis Hassabis. Highly accurate protein structure prediction with AlphaFold. July 2021.