[hamzaameer]

i just need help about that how we can analyze interaction of certain protein with the bacterial cell wall? If we can use patchdock or autodockvina than how we can convert cell wall structure into pdb file because both docking programs use pdb file. Thank you

[SunilNagpal]

i just need help about that how we can analyze interaction of certain protein with the bacterial cell wall? If we can use patchdock or autodockvina than how we can convert cell wall structure into pdb file because both docking programs use pdb file. Thank you

Hello Hamza,

You need to identify cell wall proteins with which you would like to try the docking. You may try docking with multiple cell wall proteins (if you don't know which protein to dock with) or go for the protein of interest. There are numerous pdb files for various cell wall proteins.

Hope it helps