Dear researchers
I have to reconstruct the synapse from available PDB file. The file includes MHC/endogenous peptide/TCR, but in my case there are certain condition of sequences and/or structures needs to be remodelled in silico, for which I have to:
(1) mutate certain side chain of AAs on MHC,
(2) replace endogenous peptide with the (multiple) synthetic peptide sequence(s) of interest,
(3) dock for protein-peptide(s) complex from step (1) and (2),
(4) predict drug compound interaction in the synapse (protein-ligand docking),
(5) determine validation of (each and/or whole) remodelled structure.
What procedures would you advise me to perform? What available softwares for academic (non-commercial purpose) would you recommend, please specify why you suggest such?
Regards
Hi Danny
1) For mutation - imutant 3.0 (https://services.mbi.ucla.edu/SAVES/)
2)iTASSER, Raptorx, Swiss model
3) For P-P docking- HADDOCK or ZDOCK
4)For P-L docking- Autodock, Swissdock
5) Validation through- Ramachandran plot (http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html)
Procheck- (https://services.mbi.ucla.edu/SAVES/)
Why use these software's?Because they are highly cited.
All the software's are available for free. you might have to register in some of them.
I hope it helps
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