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Abstract  Molecular shape is a useful tool for identifying small-molecules for therapeutics. Shape similarity can be found through both alignment methods, a computationally demanding approach, or through feature vector methods, computationally less demanding. Maximization of both volume overlap and various feature points makes alignment methods computationally intensive. The computational burden of alignment can be reduced by pre-aligning shapes. The recently published shapes, as is done with the  Volumetric-Aligned Molecular Shapes (VAMS) search pre-aligns the entire molecule, method. Here we introduce  and was shown to be effective as a pre-screen. The introduced method, fragment oriented molecular shape (FOMS) search, pre-aligns shapes to only a part of the shape in detail (i. e. the binding site). This eliminates the burden of aligning shapes, so large libraries consisting of millions of evaluate Fragment Oriented Molecular Shapes (FOMS), where  shapes are searched aligned based  on molecular fragments. FOMS performs equivalently or better than both VAMS and an optimizing alignment method. More significantly, FOMS enables  the scale use  of \textit{shape constraints},  a few seconds, at the loss of accuracy. FOMS has outperformed VAMS for simple protein-ligand interactions. FOMS’ performance novel method  for complex protein-ligand interactions is also explored. specifying molecular shape queries that provides the ability to perform partial shape matching and search algorithms that function on an interactive time scale.