Topic: q-bio.BM

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1. Highly accurate protein structure prediction for the human proteome

   Paper • Jul 22, 2021 • Nature • Kathryn Tunyasuvunakool, Jonas Adler, Zackary Wu, Tim Green, Michal Zielinski, Augustin Žídek, Alex Bridgland, Andrew Cowie, Clemens Meyer, Agata Laydon, Sameer Velankar, Gerard J. Kleywegt, Alex Bateman, Richard Evans, Alexander Pritzel, Michael Figurnov, Olaf Ronneberger, Russ Bates, Simon A. A. Kohl, Anna Potapenko, Andrew J. Ballard, Bernardino Romera-Paredes, Stanislav Nikolov, Rishub Jain, Ellen Clancy, David Reiman, Stig Petersen, Andrew W. Senior, Koray Kavukcuoglu, Ewan Birney, Pushmeet Kohli, John Jumper, Demis Hassabis

   The sequence of the human genome has been available for two decades, but the structures of the proteins it encodes have largely remained unknown, limiting our understanding of human health and dise...

2. Highly accurate protein structure prediction with AlphaFold

   Paper • Jul 15, 2021 • Nature • John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Demis Hassabis

   Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. We provide the first computational method that can regularly predict ...

3. Design of highly affine and specific protein binders with AlphaProteo

   Paper • Sep 5, 2024 • bioRxiv • Google DeepMind

   Designing novel proteins that bind tightly and specifically to disease-relevant targets is a fundamental challenge in drug discovery and synthetic biology. We introduce AlphaProteo, an integrated m...

4. Protein complex prediction with AlphaFold-Multimer

   Paper • Oct 4, 2021 • bioRxiv • Richard Evans, Michael O'Neill, Alexander Pritzel, Natasha Antropova, Andrew Senior, Tim Green, Augustin Žídek, Russ Bates, Sam Blackwell, Jason Yim, Olaf Ronneberger, Sebastian Bodenstein, Michal Zielinski, Alex Bridgland, Anna Potapenko, Andrew Cowie, Kathryn Tunyasuvunakool, Rishub Jain, Ellen Clancy, Pushmeet Kohli, John Jumper, Demis Hassabis

   While AlphaFold 2 achieved unprecedented accuracy in predicting the structure of single protein chains, biological functions are primarily carried out by multi-protein complexes. We present AlphaFo...

5. Accurate structure prediction of biomolecular interactions with AlphaFold 3

   Paper • May 8, 2024 • Nature • Josh Abramson, Jonas Adler, Jack Dunger, Richard Evans, John Jumper

   The interactions of proteins with other molecules, such as DNA, RNA, ligands and ions, are fundamental to biological function. Here we describe AlphaFold 3, a model that can predict the joint three...