I have a system where the protein is embedded in water box and has a non-polar interface consisting of non-polar organic molecules such as DCE. We are trying to study adsorption of protein at the interface under the effect of electric field in z-direction. The protein reaches the interface but has undergoes large conformational changes. I would like to measure the orientation angle between the helical domain of the protein and the interface (water-DCE). How do I define the normal to the surface/interface and calculate the angle?
There will likely be many different angles - not just one. However, if one part of your protein is particularly hydrophobic at its surface it will probably be the preferred 'docking' site. With a highly preferred docking site, many of the proteins molecules might approach the interface at similar angles. Once a protein makes contact with the non-polar interface, it begins to unfold either partially or completely, making angles undefinable.
Dear Neha
I prepared some power point presentation about Protein _Ligand Docking Studies.Try to see its give some idea regarding your works.
Kindly see attachments.
Thank you