Protein-peptide scoring function

HADDOCK
1

Dear Haddock team,

I would like to employ the Haddock scoring function to predict the binding affinity of a set of protein-peptide complexes. How could I do that with out the docking step?

Thanks!
Sandra

2

You can use the refinement interface - but no warranty the HADDOCK score has any correlation with binding affinity… :slight_smile:

https://wenmr.science.uu.nl/haddock2.4/refinement/1
3

Thank you very much for the information.

I was looking for the function dMM-PBSA (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5006095/) in the webserver. It is here implemented? Or could be Prodigy the most appropriate it method for BA prediction?

Thanks!
Sandra

4

Hi Sandra,

the dMM-PBSA is not implemented in the server.
Best to contact Andrea Spitaleri for the scripts.