Artificial Intelligence Stack Exchange
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Questions tagged [alpha-fold]

For questions about DeepMind's AlphaFold 1 and AlphaFold 2. AlphaFold 1 is described in the paper "Improved protein structure prediction using potentials from deep learning" (Nature volume 577, pages 706–710(2020)).

Link to original paper: https://www.nature.com/articles/s41586-019-1923-7.

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Can AlphaFold predict proteins with metals well?

There are certain proteins that contain metal components, known as metalloproteins. Commonly, the metal is at the active site which needs the most prediction precision. Typically, there is only one (or a few) metals in a protein, which contains far…
jw_
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Is AlphaFold just making a good estimate of the protein structure?

In the news, DeepMind's AlphaFold is said to have solved the protein folding problem using neural networks, but isn't this a problem only optimised quantum computers can solve? To my limited understating, the issue is that there are too many…
Aaron
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How many layers do GPT-3, AlphaFold 2, and DALL-E 2 have?

Unsuccessfully, I tried to find out the "depth" (definition below) in large neural networks such as GPT-3, AlphaFold 2, and DALL-E 2. Formally, my question is about their computational graph: consider a path from some node (a.k.a. neuron) to…
keyboardAnt
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Why is the Alphafold PAE (predicted aligned error) not symmetric?

Hi, We are running alphafold2 multimer on colab to predict the association between two proteins. It generally works fine, but we get an asymmetric PAE plot for a specific pair. Does anyone know why? I assumed these must be symmetrical ALWAYS.
NKGon
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What kind of deep learning model does latest version of AlphaFold use for protein folding problem?

I understand there are multiple versions used in AlphaFold. What kind of deep learning model does the more advanced version use? CNN, RNN, or something else? (Additionally, is there an open-source reference model for the protein folding problem?)
user781486
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