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Copy file name to clipboardExpand all lines: education/HADDOCK3/HADDOCK3-protein-peptide/index.md
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@@ -806,13 +806,17 @@ Check “Cluster partners by protein function”
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Click on "Submit".
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In a few seconds or a few minutes, ARCTIC-3D will return a set of clusters representing possible binding surfaces with respect to protein functions. Take a look at the “ARCTIC3D clustering” plot - you’ll see that some amino acids are found in the interfaces of the multiple clusters, e.g. 93-V - clusters 2, 3 and 4, while some residues are found only in a single cluster e.g. 105-R - cluster 2.
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In a few seconds or a few minutes, ARCTIC-3D will return a set of clusters representing possible binding surfaces with respect to protein functions. Take a look at the “ARCTIC3D clustering” plot: you’ll see that some amino acids are found in the interfaces of the multiple clusters, e.g. 91-F - clusters 2, 3 and 1, while some residues are found only in a single cluster e.g. 105-R - cluster 3 only.
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_**NOTE**_ this ARCTIC-3D run was performed in September 2025 and thus used strucutes available online at that time.
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With the time, new structures of MDM2_human may became available, which may lead to the change in the number and numbering of clusters.
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So if you're running ARCTIC-3D in the future, don't be surprised if the output looks a bit different!
Inspect each of the 4 clusters by clicking on the corresponding tab. Click on the “Load model” to see visual representations of the interfaces. Can you spot a difference?
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Inspect each of the 3 clusters by clicking on the corresponding tab. Click on the “Load model” to see visual representations of the interfaces. Can you spot a difference?
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What is the most relevant cluster in our case? Pay attention to the protein function!
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