A geometry-based suite of moleculardocking processes

Daniel Fischer, Shuo Liang Lin, Haim L. Wolfson, Ruth Nussinov

Research output: Contribution to journalArticlepeer-review

173 Scopus citations


We have developed a geometry-based suite of processes for molecular docking. The suite consists of a molecular surface representation, a docking algorithm, and a surface inter-penetration and contact filter. The surface representation is composed of a sparse set of critical points (with their associated normals) positioned at the face centers of the molecular surface, providing a concise yet representative set. The docking algorithm is based on the Geometric Hashing technique, which indexes the critical points with their normals in a transformation invariant fashion preserving the multi-element geometric constraints. The inter-penetration and surface contact filter features a three-layer scoring system, through which docked models with high contact area and low clashes are funneled. This suite of processes enables a pipelined operation of molecular docking with high efficacy. Accurate and fast docking has been achieved with a rich collection of complexes and unbound molecules, including protein-protein and protein-small molecule associations. An energy evaluation routine assesses the intermolecular interactions of the funneled models obtained from the docking of the bound molecules by pairwise van der Waals and Coulombic potentials. Applications of this routine demonstrate the goodness of the high scoring, geometrically docked conformations of the bound crystal complexes.

Original languageEnglish
Pages (from-to)459-477
Number of pages19
JournalJournal of Molecular Biology
Issue number2
StatePublished - 1 Jan 1995
Externally publishedYes


  • Docking of bound and unbound complexes
  • Molecular docking
  • Molecular surface matching
  • Protein-drug docking
  • Protein-protein docking

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Molecular Biology


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