Perspectives in Drug Discovery and Design

, Volume 20, Issue 1, pp 191–207

Similarity versus docking in 3D virtual screening


DOI: 10.1023/A:1008789224614

Cite this article as:
Mestres, J. & Knegtel, R.M. Perspectives in Drug Discovery and Design (2000) 20: 191. doi:10.1023/A:1008789224614


The development of similarity methods for fast flexible ligand superposition has recently received considerable attention. These efforts have brought similarity methods to a level of performance comparable to the well established protein-ligand docking methods for binding mode assessment and molecular database screening. However, the strengths and intrinsic limitations of both methodologies have been also stressed out extensively. As the number of resolved ligand-bound protein structures increases, combining ligand-based and receptor-based approaches emerges as a consensus strategy to maximally exploit the structural information available and improve the results obtained with either of the methods alone.

flexible ligand dockingflexible ligand superpositionmolecular similaritythrombinvirtual screening

Copyright information

© Kluwer Academic Publishers 2000

Authors and Affiliations

  1. 1.Molecular Design and InformaticsN.V. OrganonOssThe Netherlands
  2. 2.Molecular Design and InformaticsN.V. OrganonOssThe Netherlands
  3. 3.Vertex PharmaceuticalsOxonU.K.