Hi, all!
I had read a paper called " Insights on cross-species transmission of SARS-CoV-2 from structural modeling " ,now, I would like to repeat the experimental, but it was limited by the lab , I can only use HADDOCK web server.
So, if anyone knows what the parameters or how to do the experiment about SARS-CoV-2 RBD and ACE2 in HADDOCK web server, I want to learn parameter settings to you.
If you have the web server parameter settings file , also thank you for sending to my emai(jxyang9761@mail.ynu.edu.cn) or leave a message , I really need your help.
thanks.
Hi there,
I saw your question about our paper’s protocol on the Bioexcel forum. We didn’t use the HADDOCK web server because it didn’t support glycans at the time, so I don’t have a parameter file to give you. Nevertheless, the settings are described in our Materials and Methods section:
The initial complex models were prepared for refinement using the pdb-tools suite [38]. Each chain was separated into a different PDB file (pdb_selchain) and standardized with TER and END statements (pdb_tidy). We used HADDOCK 2.4 [39] to carry out the refinement of the models. The protein molecules were parameterized using the standard force field in HADDOCK, while the sugars were parameterized using updated parameters for carbohydrates [40]. We used a modified version of the topology generation scripts to allow automatic detection of N-linked glycans and expand the range of the interface refinement (10 Å distance cutoff). Each initial homology model was refined through 50 independent short molecular dynamics simulations in explicit solvent (solvshell = True). These refined models were then clustered using the FCC algorithm [41] with default parameters and scored using the HADDOCK score, a linear combination of van der Waals, electrostatics, and desolvation. A lower HADDOCK score is better. The top 10 models of the top scoring cluster, ranked by its average HADDOCK score, were selected as representatives of the complex.
An approximation of the protocol we used is the HADDOCK Refinement Interface webserver. It’ll be very similar, except for a shorter range for defining flexible residues. Just upload a complex of ACE2-RBD (different chains). If you want to compare directly to our results, take a complex from our dataset (available in GitHub - JoaoRodrigues/ace2-animal-models), refine it, and compare the energies.
Answering in the name of João, the first author of the paper you cite.