Paper covers a methodology for docking. It begins by retrieving protein structures from PDB, followed by protein preparation to remove or add hydrogen atoms and adjust tautomeric and protonation states. Ligands are prepared in a similar fashion. Before the actual docking, different protein sampling methods are used: rigid receptors, soft receptors, induced fit, and conformational ensembles.
After analyzing docking results for different sampling techniques, it was concluded that the best approach depends on the target. For example, if there are a lot of crystal structures available ensemble docking could be better.
Finally, it is important to carefully analyze water molecules as they may be artifact molecules caused by the crystallization technique.
Elokely, Khaled M, and Robert J Doerksen. “Docking Challenge: Protein Sampling and Molecular Docking Performance.” Journal of Chemical Information and Modeling 53, no. 8 (2013): 1934–45.
Paper covers a methodology for docking. It begins by retrieving protein structures from PDB, followed by protein preparation to remove or add hydrogen atoms and adjust tautomeric and protonation states. Ligands are prepared in a similar fashion. Before the actual docking, different protein sampling methods are used: rigid receptors, soft receptors, induced fit, and conformational ensembles.
After analyzing docking results for different sampling techniques, it was concluded that the best approach depends on the target. For example, if there are a lot of crystal structures available ensemble docking could be better.
Finally, it is important to carefully analyze water molecules as they may be artifact molecules caused by the crystallization technique.