I am discussing various charge transfer interactions of dimer conformer of thiophene-2-carboxylic acid. Also I need to dock the dimer conformer of thiophene-2-carboxylicacid with protein structures 1CX2, 1PTH and 1HPX (PDB codes). Is it possible to dock dimer structure of the molecule with protein complexes?
Herewith find the attachments of their pdb files.
The answer is obviously yes and seems technical. You need to specify which software you are using. In some, may need to redefine the pdb as having one subunit i.e. change the "B" subunit column to "A" and add to the residue number of this subunit another digit so each residue within the 'extended' A subunit will have a unique number - again this is just b/c some software doesn't know how to deal with 2 subunits.
@ilan samish
i am using autodock. is it possible with this software and how? tell me the steps. it will be a great help.
Hi,
With autodock one can do docking for the given complexes. But the procedure is some what lengthier and one can not explain it here as a chat. If you require any further clarifications will help you a lot.
- Badges
- Science method