The probes in SuperStar have been selected on the basis of diversity and availability of data. The probes available differ for CSD and PDB data. The most useful probes to start exploring a binding site are usually:
- Alcohol Oxygen: the hydroxyl group can both donate and accept hydrogen bonds, so favorable spots for hydrogen bond donors or acceptors will be detected.
- Carbonyl Oxygen: this probe will effectively indicate favorable spots for hydrogen bond acceptors.
- Uncharged NH Nitrogen: this probe will effectively indicate favorable spots for hydrogen bond donors.
- Methyl Carbon or Aromatic CH Carbon: to detect hydrophobic regions in the cavity.
It is possible for a user to include additional probe groups, by editing the file called probes.spst (located in the SuperStar root directory) which contains the probe definitions. However, the information must be present in IsoStar in order for SuperStar to use it.
Currently, IsoStar information may not be present due to a number of reasons:
- The search has not been done.
- The search has been done, but there is no information (e.g. for RNH3+ probes).
- The probe or central group will not give enough hits in the CSD (e.g. as a result of it being too large, or too uncommon).
For probes or central groups that do reside in IsoStar, the appropriate probe entries must be made in $SUPERSTAR_ROOT/suplib/probes.spst; if new central groups are added, the file $SUPERSTAR_ROOT/suplib/subfrag.spst should also be modified.