How to calculate the similairty of two protein structures in .pdb file format or how to measure the accuracy of alphafold predicted protein structure?

How to calculate the similairty of two protein structures in .pdb file format or how to measure the accuracy of alphafold predicted protein structure?

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I am new to the protein structure prediction, so the following question may sound obvious to experts in the field.

Let’s say a protein has 3d crystal structure already, and alphafold is used to predict the protein structure and generates a .pdb file. How do we know how close the predicted 3d structure is to the 3d crystal structure?


alphafold


structure


protein

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