deletions | additions       diff --git a/Abstract.tex b/Abstract.tex  index bbb1550..258b12f 100644  --- a/Abstract.tex  +++ b/Abstract.tex 
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Pharmit (\url{http://pharmit.csb.pitt.edu}) provides an online, interactive environment for the virtual screening of large compound databases using pharmacophores, molecular shape, and energy minimization. Users can import, create, and edit virtual screening queries in an interactive browser-based interface. Queries are specified in terms of a pharmacophore, a spatial arrangement of the essential features of an interaction, and molecular shape. Search results can be further ranked and filtered using energy minimization.   In addition to a number of pre-built databases of commercially available compounds, users may submit their own compound libraries for screening. Pharmit uses state-of-the-art sub-linear algorithms to provide interactive screening of millions of compounds. Queries typically take a few seconds to a few minutes depending on their complexity. This allows users to iteratively refine their search during a single session.  The abstract easy access to large chemical datasets provided by Pharmit simplifies and accelerates structure-based drug design. Pharmit is available under a dual BSD/GPL open-source license.  diff --git a/bibliography/biblio.bib b/bibliography/biblio.bib  index 352611b..6ac1685 100644  --- a/bibliography/biblio.bib  +++ b/bibliography/biblio.bib 
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@article{26085707, @article{matchpack,  title = {{Indexing Volumetric Shapes with Matching and Packing.}},  date = {2015 Apr 1},  source = {Knowl Inf Syst}, 
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}  @article{25049193, @article{vams,  title = {{Shape-based virtual screening with volumetric aligned molecular shapes.}},  date = {2014 Sep 30},  source = {J Comput Chem}, 
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}  @article{23379370, @article{smina,  title = {{Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise.}},  date = {2013 Aug 26},  source = {J Chem Inf Model}, 
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}  @article{25505090, @article{Villoutreix_2013,  doi = {10.1016/j.drudis.2013.06.013},  url = {http://dx.doi.org/10.1016/j.drudis.2013.06.013},  year = {2013},  month = {nov},  publisher = {Elsevier {BV}},  volume = {18},  number = {21-22},  pages = {1081--1089},  author = {Bruno O. Villoutreix and David Lagorce and C{\'{e}}line M. Labb{\'{e}} and Olivier Sperandio and Maria A. Miteva},  title = {{3Dmol.js: molecular visualization with WebGL.}},  date {{One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade}},  journal = {Drug Discovery Today},  }  @article{Grosdidier_2011,  doi = {10.1093/nar/gkr366},  url = {http://dx.doi.org/10.1093/nar/gkr366},  year = {2011},  month = {may},  publisher  = {2015 Apr 15},  source {Oxford University Press ({OUP})},  volume  = {Bioinformatics},  authors {39},  number  = {Rego, N {suppl},  pages = {W270--W277},  author = {A. Grosdidier and V. Zoete  and Koes, D}, O. Michielin},  title = {{{SwissDock} a protein-small molecule docking web service based on {EADock} {DSS}}},  journal = {Nucleic Acids Research},  }  @article{Wang_2014,  doi = {10.1186/1758-2946-6-28},  url = {http://dx.doi.org/10.1186/1758-2946-6-28},  year = {2014},  publisher = {Springer Science $\mathplus$ Business Media},  volume = {6},  number = {1},  pages = {28},  author = {Rego, N {Xia Wang and Haipeng Chen and Feng Yang and Jiayu Gong and Shiliang Li and Jianfeng Pei and Xiaofeng Liu and Hualiang Jiang and Luhua Lai and Honglin Li},  title = {{{iDrug}: a web-accessible and interactive drug discovery  and Koes, D}, design platform}},  journal = {Journal of Cheminformatics},  }  @article{Irwin_2009,  doi = {10.1021/jm9006966},  url = {http://dx.doi.org/10.1021/jm9006966},  year = {2015}, {2009},  month = {Apr}, {sep},  publisher = {American Chemical Society ({ACS})},  volume = {52},  number = {18},  pages = {5712--5720},  author = {John J. Irwin and Brian K. Shoichet and Michael M. Mysinger and Niu Huang and Francesco Colizzi and Pascal Wassam and Yiqun Cao},  title = {{Automated Docking Screens: A Feasibility Study}},  journal = {J. Med. Chem.},  }  @article{Koes_2012,  doi = {10.1371/journal.pone.0032839},  url = {http://dx.doi.org/10.1371/journal.pone.0032839},  year = {2012},  month = {mar},  publisher = {Public Library of Science ({PLoS})},  volume = {7},  number = {3},  pages = {e32839},  author = {David Koes and Kareem Khoury and Yijun Huang and Wei Wang and Michal Bista and Grzegorz M. Popowicz and Siglinde Wolf and Tad A. Holak and Alexander Dömling and Carlos J. Camacho},  editor = {Bin Xue},  title = {{Enabling Large-Scale Design Synthesis and Validation of Small Molecule Protein-Protein Antagonists}},  journal = {{PLoS} {ONE}},  }  @article{Koes_2012z,  doi = {10.1093/nar/gks378},  url = {http://dx.doi.org/10.1093/nar/gks378},  year = {2012},  month = {may},  publisher = {Oxford University Press ({OUP})},  volume = {40},  number = {W1},  pages = {W409--W414},  author = {D. R. Koes and C. J. Camacho},  title = {{{ZINCPharmer}: pharmacophore search of the {ZINC} database}},  journal = {Bioinformatics}, {Nucleic Acids Research},  }  @article{Rego_2014,  doi = {10.1093/bioinformatics/btu829},  url = {http://dx.doi.org/10.1093/bioinformatics/btu829},  year = {2014},  month = {dec},  publisher = {Oxford University Press ({OUP})},  volume = {31},  number = {}, {8},  pages = {1322-4},  pubmed_id {1322--1324},  author  = {25505090}, {N. Rego and D. Koes},  title = {{3Dmol.js: molecular visualization with {WebGL}}},  journal = {Bioinformatics},  }  @incollection{Koes_2015rev,  doi = {10.1007/7653_2015_46},  url = {http://dx.doi.org/10.1007/7653_2015_46},  year = {2015},  publisher = {Springer Science $\mathplus$ Business Media},  author = {David Ryan Koes},  title = {{Pharmacophore Modeling: Methods and Applications}},  booktitle = {Methods in Pharmacology and Toxicology},  }  @article{Yang_2010,  doi = {10.1016/j.drudis.2010.03.013},  url = {http://dx.doi.org/10.1016/j.drudis.2010.03.013},  year = {2010},  month = {jun},  publisher = {Elsevier {BV}},  volume = {15},  number = {11-12},  pages = {444--450},  author = {Sheng-Yong Yang},  title = {{Pharmacophore modeling and applications in drug discovery: challenges and recent advances}},  journal = {Drug Discovery Today},  }  @article{Leach_2010,  doi = {10.1021/jm900817u},  url = {http://dx.doi.org/10.1021/jm900817u},  year = {2010},  month = {jan},  publisher = {American Chemical Society ({ACS})},  volume = {53},  number = {2},  pages = {539--558},  author = {Andrew R. Leach and Valerie J. Gillet and Richard A. Lewis and Robin Taylor},  title = {{Three-Dimensional Pharmacophore Methods in Drug Discovery}},  journal = {J. Med. Chem.},  }  diff --git a/layout.md b/layout.md  index a15eed5..794897b 100644  --- a/layout.md  +++ b/layout.md 
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Abstract.tex  section_Introduction__.tex  section_Algorithms_cite_26085707_cite__.tex  section_Search__.tex  section_Library_Creation__.tex  section_Discussion__.tex  section_Acknowledgements__.tex section_Introduction_There_are_a__.tex  section_Compound_Libraries__.tex  section_Inputs_subsection_Pharmacophore_Queries__.tex  section_Search_subsection_Filters_subsection__.tex  section_Energy_Minimization_cite_smina__.tex  section_Discussion_annotations_and_iterative__.tex  section_Acknowledgements_We_thank_Charles__.tex  diff --git a/section_Acknowledgements_We_thank_Charles__.tex b/section_Acknowledgements_We_thank_Charles__.tex  new file mode 100644  index 0000000..77f0e6c  --- /dev/null  +++ b/section_Acknowledgements_We_thank_Charles__.tex 
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\section{Acknowledgements}  We thank Charles Yuan for assistance with web site design and the many early users of Pharmit for their helpful comments.  This work is funded through R01GM108340 from the National Institute of General Medical Sciences. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of General Medical Sciences or the National Institutes of Health.  diff --git a/section_Acknowledgements__.tex b/section_Acknowledgements__.tex  deleted file mode 100644  index b8d3f2b..0000000  --- a/section_Acknowledgements__.tex  +++ /dev/null 
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\section{Acknowledgements}  diff --git a/section_Algorithms_cite_26085707_cite__.tex b/section_Algorithms_cite_26085707_cite__.tex  deleted file mode 100644  index 0d0bfac..0000000  --- a/section_Algorithms_cite_26085707_cite__.tex  +++ /dev/null 
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\section{Algorithms}  \cite{26085707}\cite{25049193}\cite{23379370}\cite{25505090}  diff --git a/section_Compound_Libraries__.tex b/section_Compound_Libraries__.tex  new file mode 100644  index 0000000..3a2605a  --- /dev/null  +++ b/section_Compound_Libraries__.tex 
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\section{Compound Libraries}  diff --git a/section_Discussion__.tex b/section_Discussion__.tex  deleted file mode 100644  index c277d16..0000000  --- a/section_Discussion__.tex  +++ /dev/null 
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\section{Discussion}  diff --git a/section_Discussion_annotations_and_iterative__.tex b/section_Discussion_annotations_and_iterative__.tex  new file mode 100644  index 0000000..029ef03  --- /dev/null  +++ b/section_Discussion_annotations_and_iterative__.tex 
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\section{Discussion}  annotations and iterative search, what happens next  diff --git a/section_Energy_Minimization_cite_smina__.tex b/section_Energy_Minimization_cite_smina__.tex  new file mode 100644  index 0000000..ad8b6d7  --- /dev/null  +++ b/section_Energy_Minimization_cite_smina__.tex 
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\section{Energy Minimization}  \cite{smina}  diff --git a/section_Inputs_subsection_Pharmacophore_Queries__.tex b/section_Inputs_subsection_Pharmacophore_Queries__.tex  new file mode 100644  index 0000000..19d346f  --- /dev/null  +++ b/section_Inputs_subsection_Pharmacophore_Queries__.tex 
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\section{Inputs}  \subsection{Pharmacophore Queries}  A pharmacophore \cite{Koes_2015rev,Yang_2010,Leach_2010} defines the essential features of an interaction, such as hydrogen bond, charged, hydrophobic, or aromatic features. Importantly, a pharmacophore includes the spatial arrangement of these features and pharmacophore  \subsection{Shape Queries}  \cite{matchpack}\cite{vams}  diff --git a/section_Introduction_There_are_a__.tex b/section_Introduction_There_are_a__.tex  new file mode 100644  index 0000000..614242f  --- /dev/null  +++ b/section_Introduction_There_are_a__.tex 
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\section{Introduction}  There are a multitude of software packages and web services that assist in computer aided drug design \cite{Villoutreix_2013}, but a relative paucity of web services that support structure-based virtual screening. Those that exist, such as DockBlaster \cite{Irwin_2009} and iDrug \cite{Wang_2014}, are typically batch-processing services where the user submits a virtual screening job and receives the results hours or days later. Alternatively, advanced algorithms enable interactive time-scale searches, but existing web resources \cite{Koes_2012,Koes_2012z} are limited by a single search modality and a restricted search domain. In contrast, Pharmit provides both pharmacophore and molecular shape search modalities as well as ranking results by energy minimization, and, in addition to providing a variety of pre-built compound libraries, allows uses to upload their own compound libraries for screening.   Pharmit takes as its input structure files of a receptor and/or ligand. Structures may be provided by the user or extracted directly from the Protein Data Bank (PDB).   Pharmacophore and/or molecular shape queries are created and edited in a modern interactive interface powered by 3Dmol.js \cite{Rego_2014}, which provides high performance 3D molecular graphics without the need for plugins or Java. Once a queries is defined, the user selects and searches a compound library for matching compounds. Results are typically returned in seconds and are are displayed in-browser. A variety of filtering and ranking criteria can be applied, and hits can be further refined and ranked using energy minimization. Structure files of the query-optimized hit compounds can be downloaded, and the full session state can be saved and restored. In total, Pharmit provides a comprehensive online platform for structure-based virtual screening.  diff --git a/section_Introduction__.tex b/section_Introduction__.tex  deleted file mode 100644  index 6d8b74b..0000000  --- a/section_Introduction__.tex  +++ /dev/null 
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\section{Introduction}  diff --git a/section_Library_Creation__.tex b/section_Library_Creation__.tex  deleted file mode 100644  index d958658..0000000  --- a/section_Library_Creation__.tex  +++ /dev/null 
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\section{Library Creation}  diff --git a/section_Search__.tex b/section_Search__.tex  deleted file mode 100644  index 554bccb..0000000  --- a/section_Search__.tex  +++ /dev/null 
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\section{Search}  diff --git a/section_Search_subsection_Filters_subsection__.tex b/section_Search_subsection_Filters_subsection__.tex  new file mode 100644  index 0000000..6c2f701  --- /dev/null  +++ b/section_Search_subsection_Filters_subsection__.tex 
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\section{Search}  \subsection{Filters}  \subsection{Hit Reduction}