A case study that evaluated different docking algorithms and their ability to successfully dock ligands. The docking algorithms used did not consider protein flexibility. However, good scores were obtained, especially with a program called CDOCKER which utilizes molecular dynamics for ligand flexibility.
The study explained that one of the major problems of docking is ligand and protein flexibility. In fact, when the number of rotatable bonds increased for the ligand, the algorithms success rate decreased. Similarly, it was shown that docking accuracy falls substantially when using an average structure and that it is correlated with the degree of protein movement.
Erickson, Jon A., Mehran Jalaie, Daniel H. Robertson, Richard A. Lewis, and Michal Vieth. “Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy.” Journal of Medicinal Chemistry 47, no. 1 (2004): 45–55.
A case study that evaluated different docking algorithms and their ability to successfully dock ligands. The docking algorithms used did not consider protein flexibility. However, good scores were obtained, especially with a program called CDOCKER which utilizes molecular dynamics for ligand flexibility.
The study explained that one of the major problems of docking is ligand and protein flexibility. In fact, when the number of rotatable bonds increased for the ligand, the algorithms success rate decreased. Similarly, it was shown that docking accuracy falls substantially when using an average structure and that it is correlated with the degree of protein movement.