How can I pick a chain or a subunit to do a docking model from a multimeric enzyme on PDB. I want to do a docking model using only the active dimer and not the whole enzyme. I am sorry in advance for the simplicity of the information required but this is not my area of expertise.
As per my knowledge, it is not possible with AutoDock. You can delete unnecessary parts (water molecule, duplicate protein in the protein crystal unitcell) with the help of Discovery Studio client (it is free).... Then save it as pdb and use it for docking with AutoDock tools...
Note: do not delete any individual amino acid or chain. If so, you need to optimize the structure.
Dear Epaminondas
I have two suggestions for you:
1-when you insert a protein molecule in AutoDock , you could see and select the chain of protein and delete them with edit, as the picture that I've attached
2- pdf file, is a text file you could delete each chain in a program such as Notepad++
Hope it helps
Epaminondas Tsagkogiannis
You have two ways,
1. Just delete all the unwanted chains from your protein PDB file using any text editor like notepad++ or gedit or text editor.
2. If you are planning to do docking with full protein and target only the active site, you can restrict yourself by setting grid only on active site region from 'SELECT FROM STRING' option. But there are still chances (at least 20%-30%) that it might interact with other chains too
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