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, thrombin, virtual screening

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