I'm new in Computational Biology area. Currently I'm working out on predicting the 3D structure of my target protein. For the info, I have already built the 3D structure and undergoes some refinement analysis. Now, I am looking forward to run docking and molecular dynamic simulation for my 3D structure of the target protein. But I don't have any idea how to start the docking and MD simulation. I have already tried to study some literature. But, I'm noticed I seem lost. I would appreciate if any of you can guide me for the above matter.
thanks a lot.