Dear Marco Giulini, First of all, congratulations on your excellent participation! I am working with computational methods to elucidate the allergic mechanism triggered by polyethylene glycol used in the formulation of the Pfizer Biontech COVID-19 vaccine. I asked a question but there was no time for you to answer it in the webinar:
Through your method, it is possible to observe the change in the conformation of the binding protein-ligand IgE-Polyethylene Glycol)?
Best Regards
Hi Alexandro,
thank you for your interest! I cannot open the file unfortunately, but if you have the structure of the IGE-PEG complex you can try to refine it using our refinement interface HADDOCK Refinement Interface
Hi Marco Giulini,
I have the protein-ligand complex (AutoDock Vina) and will be refining the structure as requested. Would it be possible to analyze conformational changes through the proposed refinement?
I will be deleting the link to share the project. My drive is institutional and has blocked sharing. I will be sending it as an attachment in the post. It addresses IgE antibodies that were extensively studied during the pandemic to develop vaccines. However, some allergic reactions were triggered by some component of these formulations approved on an emergency basis. One hypothesis is that it is polyethylene glycol.
Best Regards
Alexandro Nunes
6-PROJETO (1).pdf (521 KB)
Hi,
with the refinement interface you will have access to the standard HADDOCK analysis with clustering and energetics. Of course you can also compare the refined models to the input protein-ligand complex from autodock vina (for example using pymol) to check for conformational changes occurred during refinement.
Cheers,
Marco
Excellent! Thank you for your attention and support.
Dear Marco,
I selected the best conformation using nnscore2-main. Then I deleted the other conformations from the autodock vina output file and saved it as a pdb file in autodock. And I saved it as a pdb file the receptor pdbqt file. Then I used the UCSF Chimera software to create a single file (IgE-PEG). Finally, when I submitted it to Haddock24 refinement, I did not receive an output file.
Cordially,
Alexandro
Was the submission to the server successful?
Do you have a jobID?
Dear Alexandre MJJ Bonvin,
My Haddock ID is the same as Job ID? Since no job is being processed in the dashboard. I believe the file has not been sent to the server.
Thank you for your attention,
Alexandro Nunes
then most likely something is wrong with your PDB file.
No error message reported on the top of the page?
You can share the PDB if you want us to take a look at it
Dear,
No errors message appears
I attach two files related to the IgE-PEG and IgE-PGL complexes. The ligands are Polyethylene Glycol and Polyglycerol; the receptors are 1o0v and 5mol (PDB RCSB)
Thank you for attention and support
Alexandro
Complexe5molPGL.pdb (556 KB)
Complexe1o0vPEG.pdb (528 KB)
Weird stuff in your files.
Both PDB file uses a MODEL/ENDMDL construction, making your ligand not belong to the same model (being a separate model). For example if you view it in Pymol it will only show PEG for one model, and your protein for the second. Further the ligand should have a separate chainID
Your PEG ligand has overlapping atom names. Each atom must have a unique name for HADDOCK.
Your structures have a lot of “junk”. Why keep all the crystalisation waters? Also there are glycans (as separate chains) that might not be relevant for the interaction you are focusing on. It is always good practice to visualise structures before using those for modelling tasks and remove anything unneeded.
Dear Alexandre MJJ Bonvin,
Excellent! Thank you for your attention and support.
Att.,
Alexandro Nunes