ViCi -for in silico ligand-based drug design - employs shape matching methodologies and dovetails them with further tools that help to describe the atomic makeup of a molecule and its electrostatic distribution. The software is based on the presumption that molecules of a similar size, shape and atomic makeup should interact with protein binding pockets in similar manners. Given a known macromolecular ligand, it should be possible to extract similar molecules from a large database that would interact with that molecule in a similar way, and crucially, with more affinity in some cases. The improvements in affinity can arise from the forming of new contacts, the probing of unused pockets within a binding site or the altering of molecular substructure in order to reduce conformational variability within the ligand, and the software can probe all such changes in an extremely short time-scale (a database of 8 million compounds can be screened in a few hours on a single CPU core). The newly discovered ligands should be candidates for drug development and further investigations going forward.
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