Comparison_among_predictions

• Here we are going to compare the different types of predictions by AlphaFold, Modelangelo and homology modeling with the submitted structure of the human hemoglobin with PDB ID 5ni1.

1. Import the published atomic structure: 5ni1 For details look at the Modeling tutorial and the protocol appendix

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2. Comparison among the published structure 5NI1 and AlphaFold, ModelAngelo and the homology modeling predictions: For details look at the appendix

Compare structures with: :

Recommended actions: 1.- Align any prediction to the published structure:

• mmaker #put_here_modelId to #2/A

2.- Make movements easier with:

• ~cofr

3.- Select the same part of the structure:

• sel #2/A:46-75

4.- At the end save session:

• scipionss

You should see something like this:

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Another way of superposing and comparing structures:

1. Superposition of one structure to other: For details look at the appendix

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2. Superposition of AlphaFold prediction to 5NI1 structure

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3. Superposition Result, including RMSD before and after the superposition

• QUIZ:

• What's wrong here?

• What can we do to solve it?