Comparing results between each analysis

HADDOCK
1

Hi everyone,

I´m currently working on my undegrad thesis. The general topic is evolutionary mechanisms of SARS-Cov-2. A segment of it is to evaluate the effect of mutations on the formation of RBD-ACE2 complex. First, I created the RBD homology models using sequences downloaded from the GISAID database. Now, I´m trying to understand how the different mutations on each sequence affect said complex. (Using the best cluster as the one with lowest Z-core) HADDOCK gives me the HADDOCK score, Cluster size, RMSD, Van der Waals energy, Electrostatic energy, Desolvation energy, Restraints violation energy, and Buried Surface Area. Can I use said values as a comparison between the different complexes (as in the complexes of each sequence with ACE2)?
And If so, how do I interpret each result?
Meaning, the highest /lowest HADDOCK score, and such, means a stronger or weaker interaction between the RDB-ACE2 complex?

2

I suggest you take a look at the following paper where they used HADDOCK for a similar purpose:

Rodrigues, J. P. G. L. M., Barrera-Vilarmau, S., M C Teixeira, J., Sorokina, M., Seckel, E., Kastritis, P. L., & Levitt, M. (2020). Insights on cross-species transmission of SARS-CoV-2 from structural modeling. PLoS Computational Biology, 16(12), e1008449. Insights on cross-species transmission of SARS-CoV-2 from structural modeling

1 Like
3

Thank you very much! I´m having a tough time understanding the scores and that paper could extensively help me to comprehend and correctly interpret HADDOCK results.