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Using the challenging MUV dataset we achieved highly mixed results. Some targets (eralpha, hsp90) performed poorly with all the tested shape-based methods. In these cases there likely was a lack of meaningful shape complementary between the benchmark actives and the query ligand.  optimizing method of rdkit was able to generate better than random AUCs compared to pre-alignment methods (erbeta, factor xia, fak, and hivrt)  FOMS alignment methods dramatically outperformed other methods in two cases (pka, rhok) due to correct position of fragment with key interactions. FOMS provides a rapid means of template docking \cite{Ruiz_Carmona_2014, abagyan2015icm} \cite{Ruiz_Carmona_2014,abagyan2015icm}  with shape-based scoring. Choice of fragment critical Shape constraints generally tracked or improved upon the performance of FOMS similarity ranking. For cathg, shape constraints provided the most meaningful virtual screening result as they could select for a subshape of the query ligand while the other methods must rank the full shape. 
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The expected use case for these algorithms is for scenarios where a number for fragment-oriented databases are created to enable repeated searches by multiple users investigating multiple targets, in which case the cost of database creation essentially gets amortized into insignificance.  Shape constraints provide a novel and unique method for specifying molecular shape queries. Since they are fragment oriented, they can be used to perform partial shape similarity search, a generaly challenging problem (cite). Shape constraint searches generally took well under a second making them perfect for interactive applications. Although we have investigated automatically generated shape constraints, our assumption is that intelligently designed constraints created by human experts guided by interactive analysis of a virtual screening database would substantially outperform our interaction point based constraints. This hypothesis remains untested as intuitive interfaces that allow expert users to sculpt their desired molecule need to be developed and integrated into a comprehensive virtual screening evaluation environment. diff --git a/bibliography/biblio.bib b/bibliography/biblio.bib  index 3eed2b2..769e586 100644  --- a/bibliography/biblio.bib  +++ b/bibliography/biblio.bib 
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@misc{sproxel,  key = {sproxel},  howpublished = {\url{http://code.google.com/p/sproxel/}},  title = {{sproxel, r173}},  } 
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@MISC{rdkit,  author = {Greg Landrum},  title = {{{RDK}it: Open-source cheminformatics}},  howpublished = {\url{http://www.rdkit.org}},  note = {[Online; accessed 25-October-2015]},  diff --git a/figures/all2d/all.png b/figures/all2d/all.png  index 22335cf..c59c9ad 100644  Binary files a/figures/all2d/all.png and b/figures/all2d/all.png differ