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AlphaFold (version 1 and 2) predicts (so estimates) the 3D shape of the protein from the sequence of amino acids. AlphaFold's performance is measured with the global distance test (GDT), which is a measure of similarity between two protein structures (the prediction and the ground-truth) that ranges from 0 to 100. There is a short video and a longer one (...


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Let me address first some of the things you wrote in your question: There are certain proteins that contain metal components, known as metalloproteins. Natural proteins do not ever contain metal components as far as we know. Natural proteins are composed of natural amino acids which only contain H,C,O,N,S. Selenocysteine contains Se (also a non-metal!) but ...


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The accurate answer is 'we don't know for sure'. But that said, the Deepmind article about AlphaFold 2, which won the CASP 14 competition, says this: A folded protein can be thought of as a “spatial graph”, where residues are the nodes and edges connect the residues in close proximity. This graph is important for understanding the physical interactions ...


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