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Ligands can often clash with the receptor during docking and cause unwanted placements or worse, the ligand cannot even be placed into the active site. FlexX has some useful features to monitor protein-ligand clashes and avoid excessive clashing of the ligand in the active site. The SCORE command can be used to obtain an estimate of potential protein-ligand clashes, e.g. when a ligand is going to be re-docked within the binding site for target validation. The SCORE command calculates the maximum and average volumes of clashing atoms for a reference ligand found within a crystal structure (or any docked ligands), as well as many other useful energies that contribute to the score. Therefore the reference ligand can be analyzed for the amount of clashes that already exist in the crystal structure giving an indication on the amount of clashes expected within future docking solutions.
The steps to overcome extensive protein-ligand clashes are described here:
- Read in a reference ligand, the ligand to be docked and a receptor as normal. The reference ligand must be in its crystal conformation. Then enter the DOCKING directory followed by the ANALYZE sub-directory and type SCORE REF Y Y N which will give you a feel for the amount of clashes that can be expected when you re-dock the ligand at a later stage. A similar output to the one below will appear :
Score contributions
dG_0 : 5.400 kJ/mol
dG_rot : 22.400 kJ/mol
dG_match : -17.918 kJ/mol
dG_lipo : -17.166 kJ/mol
dG_ambig : -5.947 kJ/mol
dG_clash : 6.616 kJ/mol
dG_total : -6.615 kJ/mol
Protein-Ligand overlap
max. atom-atom : 0.660 A^3
ave. atom overlap: 0.145 A^3
RMSD to reference : 0.000 A
(the maximum and average volume overlap are highlighted)
If the maximum atom-atom overlap is too large (i.e. > 2.5Å3), the user can adjust the parameter MAX_OVERLAP_VOL accordingly, which is a threshold value for the overlap/clashing test between the protein and ligand in FlexX. Please note that hydrogen atoms are not taken into account in this calculation using the parameters ("Y"es and "N"o as above). The default value for MAX_OVERLAP_VOL is 2.5Å3, and increasing this parameter creates a "softer" docking approach, very high values are equivalent to turning off the overlap test. Thus, if you are trying to dock a ligand into a tight but well defined binding site and you think your docking is failing due to clashes then maybe a simple change to the MAX_OVERLAP_VOL parameter will permit docking.
- Check whether the docking is failing due to clashing conformations. This can be done by viewing the output from FlexX during the incremental construction phase.
>> Fragment 2
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# of complete placements : 0
# of expanded conformations : 60
# of clashing conformations : 60
# of eliminated clashes : 0
# of filtered placements : 0
# of pharm filtered placements : 0 ( 0| 0| 0)
# placements before clustering : 0
# resulting dock entries : 0
energy cutoff (k best solution): inf
>> WARNING: No solution found.
- Now type SET, generally in any of the menus of FlexX you will be able to change a range of variables with the SET command.
- Select the MAX_OVERLAP_VOL parameter and set it to a desired value within the range of 0.0Å3 - 100.0Å3. Remember the higher the value the "softer" the docking approach and the more clashes are permitted.
- Now re-run the docking experiment with your adjusted clash computation.
Please note that this parameter can also be changed if your complex is not completely failing and you are trying to optimize the results of FlexX. Thus manipulation of this parameter can be undertaken if you notice high levels of clashing during incremental construction.
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© BioSolveIT GmbH, 2010 |
Last modified Monday, 05. Jul 2010 13:57 CEST by WebMaster |
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