Can you suggest me some similar tools and tutorials for the same.
I have a protein with enzymatic activity. I wish to analyze the active site cavity size and SASA variations/fluctuations throughout the simulation by analyzing the trajectory.
In MDpocket, the drawback is user cannot define the cavity (Am I right with my statement?). It detects the cavities using fpocket and performs analysis. This is a great limitation and introduces unspecificity during the course of the analysis. Kindly give your valuable suggestions.