What is AutoDock?
- AutoDock is the automated molecular docking software package that has been distributed to academics and non-profit research institutes free-of-charge since 1990.
- AutoDock offers a variety of search algorithms to explore a given docking problem. These include Monte Carlo Simulated Annealing (SA); a Genetic Algorithm (GA); and a hybrid local search GA, also known as the Lamarckian Genetic Algorithm (LGA). In general, the LGA performs the best out of SA, GA, and LGA, in finding the lowest energy of the system.
- AutoDock 3 and later versions use a linear free energy model of molecular mechanics terms including van der Waals non-bonded interactions, directional hydrogen bonding, screened Coulombic electrostatics, and an atomic solvation parameter-based desolvation free energy term. There is also an empirical term that estimates the loss of torsional entropy of the ligand upon binding.
What is new in AutoDock 4?
- You can read more about version 4 on the AutoDock4 page.