Virtual screening setup

From Library Preparation to Ligand-based and Structurebased Virtual Screening

Alessandro Pedretti
Department of Pharmaceutical Sciences, University of Milan

In the drug discovery process, virtual screening is one of the most powerful computational approaches that can be used to identify potential new ligands able to interact with a biological target. Since its capabilities in finding hit compounds are widely accepted, this method is largely applied in academic and industrial research fields. However, the quality of the results is strictly related not only to the screening technique (ligand- or structure-based) and the setup of the calculation, but also to the ligand libraries that must span the largest chemical to increase the possibility to find molecules with an optimal interaction with the biological target. Moreover, structure-based screenings and calculations of conformational-dependent molecular properties such as those for ligand-based screenings require the 3D structure of the molecules included in the library and for this reason the building of a library is a key phase in the screening process.

During this workshop, it will be explained how to build libraries by including 3D structures of potential ligands in SQL databases starting from different data types (2D SDF files, SMILES strings, images, etc) and how to setup structure-based virtual screenings with different programs by using the graphic interface of VEGA ZZ software1,2.


1. Pedretti, A.; Villa, L.; Vistoli, G., "VEGA - An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script" programming", J. Comput. Aided. Mol. Des. 2004, 18, 167-173.
2. Pedretti, A.; Villa, L.; Vistoli, G., "VEGA: a versatile program to convert, handle and viusualize molecular structure on windows-based PCs", J. Mol. Graph., 2002, 21, 47-49.