Docking and Virtuel screening

Docking programs are algorithms used to predict the structure of the complex formed between a protein and a putative ligand. For practical purposes the protein structure is held rigid (frosen) and the problem is reduced to predicting the conformation of the bound ligand which is reffered to as a pose. Since most ligands are flexible and have many low energy conformations, several poses must be evaluated for each ligand. This evaluation is done by a scoring algorithm and can be regarded as a calculation of the binding constant between the protein and the evaluated ligand conformation.
Structure based virtuel screening is docking of either commersially available compounds, or compounds that can be made using parallel synthesis or combinatorial chemistry. In this way a large number (1000-1000000) of compounds are screened and only the highest scoring are purchased ore synthesised. Experience shows that virtuel screening can typically improve hit rates (the number of active compounds) by a factor of 3-100.
This example show a protein (HIV protease) with several HIV protease inhibitors docked. Only the top 25 poses are shown. Each ligand may apear up to 10 times. You can turn ON/OFF the protein and ligand surfaces to better evaluate the steric fit.

Active site surface
Pose 1
Pose 2
Pose 3
Pose 4
Pose 5
Pose 6
Pose 7
Pose 8
Pose 9
Pose 10
Pose 11
Pose 12
Pose 13
Pose 14
Pose 15
Pose 16
Pose 17
Pose 18
Pose 19
Pose 20
Pose 21
Pose 22
Pose 23
Pose 24
Pose 25

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Molecular Mechanics (MM)

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