site2spheres

• Generate complete, optimal set of 1,000 - 10,000 overlapping, variable radius spheres tangent to protein atoms in 30 - 90 seconds using Yeates' inversive geometry algorithm (T. Yeates, J. Mol. Bio., 249, 804-814, 1995). This algorithm analytically constructs the maximal sphere tangent to four other spheres.

 
• Filter spheres by their LIGSITE solvent-accessibility score.

 
• Merge remaining closely overlapped spheres and remove redundant spheres.

 
• Cluster remaining spheres and sort clusters by their LIGSITE score to output 50-100 spheres per site.

 
• Optionally specify macromolecule residues and atoms to define proximity to included or excluded sites. Sphere generation is fast enough to apply iteratively.
   
• Binding site is in cluster 1 in 94/123 cases
  Binding site is in cluster 2 in 15/123 cases
  Binding site is in clusters 3-5 in remaining cases.

 
• RubiconDock accepts multiple potential binding sites.