Molecular docking is the computer- aided prediction of a binding mode of two macromolecules or a small molecule to
In the prediction process we take into consideration geometrical match, as well as evolutionary conservation of the binding pocket or interface, as well as electrostatic and hydrophobic match.
We predict the binding mode of small molecules (such as drugs) to a protein with known 3D structure. It is possible to calculate binding affinity.
We predict the preffered binding mode of two (or more) proteins, or protein-DNA complex.
It is important to note that docking methods assume binding.
They are not designed to asnwer the question "Will these two proteins bind each other?" However, it is possible to compare binding affinity of various complexes.
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