Fragment-based conformational search

In the MOE environment, molecules are stored in a database with their associated set of conformations. Several methods can be applied to expand the conformational space of organic molecules ranging from molecular dynamics to stochastic methods and systematic search. A fragment-based high-throughput... 

Force field based methods also have merits. The main difficulties lie in their slowness, which hinders the search of a fragment s conformational space... 

Shape. Pharmacophores capture the key features of intermolecular interactions. However, they do not explicitly capture the shape and volume of the ligand, even if this is crudely implied by the largest four-point pharmacophore exhibited, and the totality of potential pharmacophores exhibited across a range of conformations encodes shape fragments. Hahn (47) has described a method for three-dimensional shape-based searching implemented in the Catalyst program. Seven... 

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