Perspectives in Drug Discovery and Design, 20: 191–207, 2000. KLUWER/ESCOM © 2000 Kluwer Academic Publishers. Printed in the Netherlands. Similarity versus docking in 3D virtual screening JORDI MESTRES * and RONALD M.A. KNEGTEL ** Molecular Design and Informatics, N.V. Organon, 5340 BH Oss, The Netherlands Summary. 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. Key words: flexible ligand docking, flexible ligand superposition, molecular similarity, throm- bin, virtual screening Introduction Virtual screening (VS, also referred to as molecular database screening or in silico screening) is the process of reducing a library containing an unman- ageable number of compounds (available or virtual) to a limited number of potentially promising compounds for the target (or target family) of interest by means of computational techniques [1]. The rapid advance of new tech- nologies such as combinatorial chemistry [2] and high-throughput screening [3] offers the possibility of synthesizing and testing hundreds of thousands of compounds. However, as the pressure on pharmaceutical companies to deliver more targets to the lead discovery pipeline augments, VS will increasingly become a valuable strategy for prioritizing compounds for screening. This should provide an optimum balance between the possibility of still screening every single target while maintaining time, cost, and waste of compounds at a reasonable level. * To whom correspondence should be addressed. E-mail: j.mestres@organon.oss.akzonobel.nl ** Present address: Vertex Pharmaceuticals, 88 Milton Park, Abingdon, Oxon OX14 4RY, U.K.