Can anyone please help me in understanding the importance of torsion angle analysis and torsion potential analysis of a ligand while analyzing a protein-ligand simulation trajectory. How can the analysis be done and presented while writing in discussion?
Rotation around a given bond may reflect some conformational sampling of the ligand, e.g. the position of rings or other relevant functional groups relative to one another. A simple way to quantify this (in some cases) is to plot the time series and/or distribution of a given dihedral angle that reflects such sampling.
Sometimes, in polymers these dihedral distribution can be used to understand the transition temperature for ordering of chains. As Justin said, it is mainly for conformational analysis if any particular conformation is preferred over another.
Thank you Justin and Gourav for your insights.
I am trying to relate the torsion potential energy of a rotatable bond with its torsion angle throughout the simulation. At particular angle, the torsion potential is high and at some other angle it is almost zero. How to relate this in terms of ligand characteristics. In my study I want to show this particular ligand is with good binding stability at the protein active site which has also been proven in in-vitro studies. Can you people please help me out in understanding this?
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