SuperStar

Protein-ligand interactions prediction (CSD)

Description

SuperStar is a program for generating maps of interaction sites in proteins or around small molecules using experimental information about intermolecular interactions. The interaction maps that SuperStar generates are therefore fully knowledge-based.

SuperStar retrieves its data from IsoStar, CCDC's interaction database. IsoStar contains information about non-bonded interactions from both the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB).

SuperStar features:

• Fast generation of maps (less than 1 minute per binding site)
• Search possible binding sites in a protein
  
• Use of either CSD or PDB data
• Metal coordination data
• Stand alone graphical user interface (hermes) and seamless interface to SYBYL
• Expert command-line interface
• Built-in cavity detection that selects residues automatically
• Knowledge-based approach: all results can be traced back to experimentally observed geometries of interaction
• Application of parameterised Gaussian functions for speeding up calculations
• Choice of 14 CSD probes and 6 PDB probes selected for diversity and data availability (including a water probe)
• Visualisation through 3D maps, Connolly surfaces, scatterplots, and pharmacophore fitting points
• Extensive validation on a test set of 305 protein-ligand complexes from the PDB and this is available for download.

Usage

To start using SuperStar (like all other CSD-package software) in Hippu give:

module load ccdc

and then run Hermes, which is the graphical interface to SuperStar by

hermes

and choose SuperStar from the Calculate menu. Alternatively, if you have an input file (.ins) available, you can start superstar directly from the command line with

superstar myinput.ins

More information

Please see SuperStar web page at Cambridge crystallographic Database for manuals and more information.