Clashes

The definition of clashes is somewhat problematic for purposes of pose prediction. In general, serious clashes where interpenetration with the protein should be avoided at all costs. However, when docking into a rigid protein that does not have the appropriate conformation, rigid docking ignores that fact that the active site may adopt a conformation suitable to the posed ligand.

The posit application deals with clashes by allowing the user to specify three allowable clash levels with cutoffs taken by analyzing various ligands in deposited in the protein data bank (RSCB).

Allowed Clash Description
noclashes No clashes are allowed. Actually there is a little wiggle room here less than 0.2 Ångström penetration is not considered a clash.
mildclashes Mild clashes are allowed ( >= 0.2 Ångström < 0.65 Ångström interpenetration)
allclashes All clashes are allowed.

If a pose clashes, it is not thrown away, it is written to the clashed molecule file. Clashed molecule files hold ligands with decent probability when compared to the bound ligand, but have unallowable clashes with the protein.

Clashing can also affect the known bound ligand. When making a receptor for posit, if a bound ligand clashes with the protein beyond the allowable clash level, a warning will be given and the receptor will not be generated. In this case, the appropriate command line switch will be given in order to generate the receptor. It is advisable to visually inspect clashing complexes (and electron density if available) to decide whether the clash is acceptable or not.

Note that if a receptor is made with the -allclashes option, posit should also be run with the same option or the -clash file should be specified on the command line.

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