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AutoDock is used to perform computational molecular docking of small molecules to proteins, DNA, RNA and other important macromolecules, by treating the ligand and selected parts of the target as conformationally flexible. It uses a scoring function based on the AMBER force field, and estimates the free energy of binding of a ligand to its target. Novel hybrid global-local evolutionary algorithms are used to search the phase space of the ligand-macromolecule system. We describe here the fundamental science that AutoDock is based on. Principles, laws and equations can be found in this section. We also present some applications of AutoDock from the published literature.

AutoDock by garrett — last modified 2007-03-23 17:58
AutoDock was the first docking program to model the ligand with full conformational flexibility. The first version was written in Prof. Arthur J. Olson's Laboratory in 1989-1990, in FORTRAN-77, by ...
Applications — — last modified 2007-07-31 17:01
Blind Docking
Equations by morris — last modified 2009-07-16 12:37
Here is a summary of the equations used in the AutoDock force field.
Coulomb's Law by morris — last modified 2006-08-23 13:41
Charles Augustin de Coulomb (1736-1806) formulated the inverse square law in 1785 that describes how the force between two point charges varies according to the separation between them. Joseph Priestly, who was not only one of the discoverers of oxygen, but who also wrote a comprehensive treatise on electricity, anticipated this result some two decades before Coulomb.
Dimensional Analysis by morris — last modified 2006-08-23 13:41
There are five fundamental dimensions, quantities that can be readily measured in experiments. Constants like π have no dimensions, they are said to be dimensionless.
Desolvation Free Energy Term in AutoDock 4 by morris — last modified 2007-03-23 17:43
This page summarizes the AutoDock 4 desolvation free energy term, which is based on new atomic solvation parameters which depend on the absolute partial charge on the atom. This page also describes how the desolvation free energy grid map is calculated.

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