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% introduction and background  \hyphenation{mol-e-cules}  Molecular shape is a fundamental concept in medicinal chemistry \cite{Nicholls2010}, and shape-based virtual screens have successfully identified novel inhibitors.\cite{RushIII2005,McMasters2009,Muchmore2006,Naylor_2009}  Shape is used both to assess the similarity of a candidate molecule to a set of known actives and to evaluate the complementarity of a molecular shape to the shape of the binding site on the target receptor. Here we describe a novel method for \textit{exactly} specifying shape constraints for querying a large library of molecular shapes. The shape constraints are derived from both the receptor, which describes where a molecule cannot be, and from the shape of a known binder, which describes where the molecule should be.