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Equation 5 · How AI for Science and Medicine Actually Works

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ϵ\epsilon

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a random quantity drawn from a standard normal distribution. Read the equation part by part below; each part has a contextual explanation and a link to its mathematical background.

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ϵ\epsilon

Symbol epsilon

a random quantity drawn from a standard normal distribution.

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with ϵ\epsilon drawn from a standard normal distribution and fθf_\theta the trained network. Generating a structure then means starting from coordinates that are almost pure noise and repeatedly applying the trained denoiser, each pass nudging the atoms closer to a physically coherent arrangement, across many scales at once — from the local geometry of a single ring to the global fold of an entire complex [ 2 ] . Both AlphaFold2 and AlphaFold3 were trained on structures deposited in the Protein Data Bank; AlphaFold3’s training data was cut at structures released before 30 September 2021, supplemented by sequence databases including UniRef90, Uniclust30, and BFD, and RNA-specific databases…
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with ϵ\epsilon drawn from a standard normal distribution and fθf_\theta the trained network. Generating a structure then means starting from coordinates that are almost pure noise and repeatedly applying the trained denoiser, each pass nudging the atoms closer to a physically coherent arrangement, across many scales at once — from the local geometry of a single ring to the global fold of an entire complex [ 2 ] . Both AlphaFold2 and AlphaFold3 were trained on structures deposited in the Protein Data Bank; AlphaFold3’s training data was cut at structures released before 30 September 2021, supplemented by sequence databases including UniRef90, Uniclust30, and BFD, and RNA-specific databases including Rfam and RNAcentral [ 2 ] .

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