I performed mutagenesis on a protein (1-3 mutations max), and I wanted to use HADDOCK. I used the same parameters for every variant + the WT protein. Can I compare average HADDOCK cluster score between different jobs (variants) to the wild type if the parameters are identical?
Dear Abdullah.
To be able to compare clusters, you need to make sure you obtained the same (more or less) conformations.
But because cluster IDs may vary between runs, you cannot compare HADDOCK score of the same cluster IDs.
If you install and use Haddock3, you can use the [alascan] module (see here the user manual for this module: Analysis - HADDOCK3 User Manual) to perform those mutations and evaluate the difference in Haddock score, which will lead to results easier to analyse and compare.
Unfortunately, HADDOCK3 is still only available for local installations and not yet proposed as a web service.
Hope this helps,
Cheers,
Victor
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This is indeed a reasonable approach.
But you might not need to run full docking for this.
If you have a structure or good model of the complex, you could using the refinement interface of the server to compare WT with various mutants.
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