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Back to 🔬 Why AlphaFold Didn't Solve Protein Folding — Pushmeet Kohli, Google DeepMind & Sal Candido, Biohub, with Pushmeet Kohli & Sal Candido.

Did AlphaFold Solve Protein Folding?

Pushmeet Kohli says the protein folding problem has been solved only at a conceptual level. There have been some advances, and a protein's shape might change depending on the context. Science operates by isolating one thing and then making progress step by step.

Proteins are not blocks, and they do not act as blocks. He says he calls proteins the building blocks all the time, and he does not believe it. Proteins are extremely complex and disordered. He and John Jumper used to ask what they were trying to solve. The true ground state proteins take is unknown, and so is the actual distribution of structure proteins take.

What the work did was take a structure someone deposited in the PDB and replicate it until the result was the same structure. That turned out to be useful. It does not mean protein dynamics are understood.

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Transcript

🔬 Why AlphaFold Didn't Solve Protein Folding — Pushmeet Kohli, Google DeepMind & Sal Candido, Biohub ·

Latent Space: The AI Engineer Podcast

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  1. What Is the Bitter Lesson for Biological Data?Sal Candido says there is a bitter lesson for data, but scaling laws are not everywhere and they do not always exist.
  2. Why Should a Biology Problem Come Before the Model?Pushmeet Kohli says the problem comes first, because treating yourself as only a modeler or only a data person can make the work fail.
  3. Why Does AlphaFold Need a Calibrated Confidence Score?Pushmeet Kohli says AlphaFold 2 needs a calibrated uncertainty measure, because an uncalibrated PLDDT score would present a very, very confident answer that…
  4. Why Does Biohub Chase a 10x Approach?Sal Candido says Biohub chases a 10x approach because the mission is to cure all disease, and a 10x goal shows solutions a 10% goal leaves hidden.

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