title: Rigid substructure search.
abstract: BACKGROUND
  Identifying the location of binding sites on proteins is of fundamental importance for a wide range of applications, including molecular docking, de novo drug design, structure identification and comparison of functional sites. Here we present Erebus, a web server that searches the entire Protein Data Bank for a given substructure defined by a set of atoms of interest, such as the binding scaffolds for small molecules. The identified substructure contains atoms having the same names, belonging to same amino acids and separated by the same distances (within a given tolerance) as the atoms of the query structure. The accuracy of a match is measured by the root-mean-square deviation or by the normal weight with a given variance. Tests show that our approach can reliably locate rigid binding scaffolds of drugs and metal ions.
  
  
  METHODS
  We provide this service through a web server at http://erebus.dokhlab.org.
authors: Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599-7260, USA.
authors: David
authors: D
authors: Shirvanyants
authors: Anastassia N
authors: AN
authors: Alexandrova
authors: Nikolay V
authors: NV
authors: Dokholyan
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D030562:Databases, Protein; D015195:Drug Design; D020407:Internet; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins