SuperStar - Scientific FAQs

Scientific FAQs

How do I obtain SuperStar?
Can I use SuperStar in conjunction with other modeling software packages?
Is it possible to use SuperStar for database screening?
Is it possible to include any additional probe groups?
How do I reference SuperStar?

How do I obtain SuperStar?

SuperStar is only available to CSD subscribers, it is fully knowledge-based and retrieves its data from IsoStar, CCDC's database of nonbonded interaction which is distributed as part of the CSD System. For those interested in purchase, a free evaluation copy of SuperStar is normally available for a period of 60 days. A password and userid are required to be able to download the software: these can be obtained by contacting the CCDC at the following address:

Can I use SuperStar in conjunction with other modeling software packages?

SuperStar has an interface via Hermes. It features easy selection of calculation settings, and offers much control over the display of multiple maps.

In addition, Superstar has a dedicated SYBYL (http://www.tripos.com) graphical user interface that allows the user to calculate SuperStar fields and view them within the SYBYL environment. SuperStar fields can also be viewed using Insight (http://www.accelryrs.com/insight/), for further information please refer to the SuperStar Online documentation.

SuperStar also features a command line interface for optimal flexibility.

Is it possible to use SuperStar for database screening?

Yes. SuperStar maps can be expressed as a set of pharmacophore points, which highlight the key interactions represented within the map. Pharmacophore points are derived from the map using a Gaussian fitting procedure and results are displayed as discrete points within the three-dimensional SuperStar map. The position of these points are stored in a file and can, for example, be used to set up pharmacophore-based searches.

Is it possible to include any additional probe groups?

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 donor and acceptor will be detected.

Carbonyl Oxygen: this probe will effectively indicate favorable spots for hydrogen bond acceptors.

Methyl Carbon or Aromatic CH Carbon: to detect hydrophobic regions in the cavity.

It is possible for a user to include additional probe groups. In the SuperStar root directory, there is a file called probes.spst 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 (occurs eg. for RNH₃⁺ probes)
The probe or central group will not give enough hits in the CSD (eg. 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.

How do I reference SuperStar?

SuperStar References

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