Prev
18.5 ICM X-Ray AutoFit - Automated Model Building into Density
Next

The ICM X-Ray AutoFit is an automated method to fit a ligand into electron density. The tool combines the powerful ICM docking algorithm with an electron density fitting function.

The input for ICM X-Ray AutoFit is an electron density map in CCP4 format, the protein recpeptor and ligand which can either be drawn or imported into ICM.

Theory

The ICM X-Ray AutoFit method includes the following features:

NOTE: Density from the receptor is automatically filtered out from the analysis. In the picture shown above the green map represents attractive potential.

The method generates multiple hits for each ligand with a score assigned. It has been demonstrated that improved ligand receptor interactions can be determined by the ICM X-Ray AutoFit method compared to published crystal structures.

In the figure shown below the interaction between Gleevec and Syk kinase is shown. The white carbon atoms are the published ligand pose and the yellow carbon ligand is the result of ICM which gives a better fit to the density.

Instructions

How to run the ICM X-Ray AutoFit.


Prev
Vls analysis
Home
Up
Next
Protein-Protein Docking