@article{matchpack,
  title = {{Indexing Volumetric Shapes with Matching and Packing.}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/26085707}{26085707}] [PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4465823}{PMC4465823}] [doi:\href{http://dx.doi.org/10.1007/s10115-014-0729-z}{10.1007/s10115-014-0729-z}]},
  date = {2015 Apr 1},
  source = {Knowl Inf Syst},
  authors = {Koes, DR and Camacho, CJ},
  author = {Koes, DR and Camacho, CJ},
  year = {2015},
  month = {Apr},
  journal = {Knowl Inf Syst},
  volume = {43},
  number = {},
  pages = {157-180},
  pubmed_id = {26085707},
}


@unpublished{PyMOL,
  annote = {PyMOL The PyMOL Molecular Graphics System, Version 1.8, Schr{\"o}dinger, LLC.},
  author = {{Schr\"odinger, LLC}},
  date-added = {2010-08-19 17:29:55 -0400},
  date-modified = {2015-12-22 18:04:08 -0400},
  month = {November},
  title = {{The {PyMOL} Molecular Graphics System, Version~1.8}},
  year = {2015},
}


@misc{moe,
  title = {{Molecular Operating Environment (MOE)}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/19075767}{19075767}]},
  author = {{Chemical Computing Group}},
  year = {2016},
  publisher = {Chemical Computing Group Inc. Montreal, QC},
}


@article{vams,
  title = {{Shape-based virtual screening with volumetric aligned molecular shapes.}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/25049193}{25049193}] [PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140985}{PMC4140985}] [doi:\href{http://dx.doi.org/10.1002/jcc.23690}{10.1002/jcc.23690}]},
  date = {2014 Sep 30},
  source = {J Comput Chem},
  authors = {Koes, DR and Camacho, CJ},
  author = {Koes, DR and Camacho, CJ},
  year = {2014},
  month = {Sep},
  journal = {J Comput Chem},
  volume = {35},
  number = {},
  pages = {1824-34},
  pubmed_id = {25049193},
}


@article{smina,
  title = {{Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise.}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/23379370}{23379370}] [PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726561}{PMC3726561}] [doi:\href{http://dx.doi.org/10.1021/ci300604z}{10.1021/ci300604z}]},
  date = {2013 Aug 26},
  source = {J Chem Inf Model},
  authors = {Koes, DR and Baumgartner, MP and Camacho, CJ},
  author = {Koes, DR and Baumgartner, MP and Camacho, CJ},
  year = {2013},
  month = {Aug},
  journal = {J Chem Inf Model},
  volume = {53},
  number = {},
  pages = {1893-904},
  pubmed_id = {23379370},
}


@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 = {{One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/23831439}{23831439}] [doi:\href{http://dx.doi.org/10.1016/j.drudis.2013.06.013}{10.1016/j.drudis.2013.06.013}]},
  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 = {Oxford University Press ({OUP})},
  volume = {39},
  number = {suppl},
  pages = {W270--W277},
  author = {A. Grosdidier and V. Zoete and O. Michielin},
  title = {{{SwissDock} a protein-small molecule docking web service based on {EADock} {DSS}}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/21624888}{21624888}] [PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125772}{PMC3125772}] [doi:\href{http://dx.doi.org/10.1093/nar/gkr366}{10.1093/nar/gkr366}]},
  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 and Business Media},
  volume = {6},
  number = {1},
  pages = {28},
  author = {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 design platform}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/24955134}{24955134}] [PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046018}{PMC4046018}] [doi:\href{http://dx.doi.org/10.1186/1758-2946-6-28}{10.1186/1758-2946-6-28}]},
  journal = {Journal of Cheminformatics},
}


@article{Irwin_2009,
  doi = {10.1021/jm9006966},
  url = {http://dx.doi.org/10.1021/jm9006966},
  year = {2009},
  month = {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}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/19719084}{19719084}] [PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745826}{PMC2745826}] [doi:\href{http://dx.doi.org/10.1021/jm9006966}{10.1021/jm9006966}]},
  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}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/22427896}{22427896}] [PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299697}{PMC3299697}] [doi:\href{http://dx.doi.org/10.1371/journal.pone.0032839}{10.1371/journal.pone.0032839}]},
  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}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/22553363}{22553363}] [PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394271}{PMC3394271}] [doi:\href{http://dx.doi.org/10.1093/nar/gks378}{10.1093/nar/gks378}]},
  journal = {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--1324},
  author = {N. Rego and D. Koes},
  title = {{3Dmol.js: molecular visualization with {WebGL}}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/25505090}{25505090}] [PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393526}{PMC4393526}] [doi:\href{http://dx.doi.org/10.1093/bioinformatics/btu829}{10.1093/bioinformatics/btu829}]},
  journal = {Bioinformatics},
}


@article{Sanders_2012,
  doi = {10.1021/ci2005274},
  url = {http://dx.doi.org/10.1021/ci2005274},
  year = {2012},
  month = {May},
  publisher = {American Chemical Society ({ACS})},
  volume = {52},
  number = {6},
  pages = {1607--1620},
  author = {Marijn P. A. Sanders and Arménio J. M. Barbosa and Barbara Zarzycka and Gerry A.F. Nicolaes and Jan P.G. Klomp and Jacob de Vlieg and Alberto Del Rio},
  title = {{Comparative Analysis of Pharmacophore Screening Tools}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/22646988}{22646988}] [doi:\href{http://dx.doi.org/10.1021/ci2005274}{10.1021/ci2005274}]},
  journal = {Journal of Chemical Information and Modeling},
}


@incollection{Koes_2015rev,
  doi = {10.1007/7653_2015_46},
  url = {http://dx.doi.org/10.1007/7653_2015_46},
  year = {2015},
  publisher = {Springer Science and Business Media},
  author = {David Ryan Koes},
  title = {{Pharmacophore Modeling: Methods and Applications}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/21521148}{21521148}]},
  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}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/20362693}{20362693}] [doi:\href{http://dx.doi.org/10.1016/j.drudis.2010.03.013}{10.1016/j.drudis.2010.03.013}]},
  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}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/19831387}{19831387}] [doi:\href{http://dx.doi.org/10.1021/jm900817u}{10.1021/jm900817u}]},
  journal = {J. Med. Chem.},
}


@article{Gaulton_2011,
  doi = {10.1093/nar/gkr777},
  url = {http://dx.doi.org/10.1093/nar/gkr777},
  year = {2011},
  month = {Sep},
  publisher = {Oxford University Press ({OUP})},
  volume = {40},
  number = {D1},
  pages = {D1100--D1107},
  author = {A. Gaulton and L. J. Bellis and A. P. Bento and J. Chambers and M. Davies and A. Hersey and Y. Light and S. McGlinchey and D. Michalovich and B. Al-Lazikani and J. P. Overington},
  title = {{{ChEMBL}: a large-scale bioactivity database for drug discovery}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/21948594}{21948594}] [PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245175}{PMC3245175}] [doi:\href{http://dx.doi.org/10.1093/nar/gkr777}{10.1093/nar/gkr777}]},
  journal = {Nucleic Acids Research},
}


@article{Kim_2015,
  doi = {10.1093/nar/gkv951},
  url = {http://dx.doi.org/10.1093/nar/gkv951},
  year = {2015},
  month = {Sep},
  publisher = {Oxford University Press ({OUP})},
  volume = {44},
  number = {D1},
  pages = {D1202--D1213},
  author = {Sunghwan Kim and Paul A. Thiessen and Evan E. Bolton and Jie Chen and Gang Fu and Asta Gindulyte and Lianyi Han and Jane He and Siqian He and Benjamin A. Shoemaker and Jiyao Wang and Bo Yu and Jian Zhang and Stephen H. Bryant},
  title = {{{PubChem} Substance and Compound databases}},
  journal = {Nucleic Acids Res},
}


@article{Rappe_1992,
  doi = {10.1021/ja00051a040},
  url = {http://dx.doi.org/10.1021/ja00051a040},
  year = {1992},
  month = {Dec},
  publisher = {American Chemical Society ({ACS})},
  volume = {114},
  number = {25},
  pages = {10024--10035},
  author = {A. K. Rappe and C. J. Casewit and K. S. Colwell and W. A. Goddard and W. M. Skiff},
  title = {{{UFF} a full periodic table force field for molecular mechanics and molecular dynamics simulations}},
  journal = {J. Am. Chem. Soc.},
}


@article{Ebejer_2012,
  doi = {10.1021/ci2004658},
  url = {http://dx.doi.org/10.1021/ci2004658},
  year = {2012},
  month = {May},
  publisher = {American Chemical Society ({ACS})},
  volume = {52},
  number = {5},
  pages = {1146--1158},
  author = {Jean-Paul Ebejer and Garrett M. Morris and Charlotte M. Deane},
  title = {{Freely Available Conformer Generation Methods: How Good Are They?}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/22482737}{22482737}] [doi:\href{http://dx.doi.org/10.1021/ci2004658}{10.1021/ci2004658}]},
  journal = {Journal of Chemical Information and Modeling},
}


@article{O_Boyle_2011,
  doi = {10.1186/1758-2946-3-33},
  url = {http://dx.doi.org/10.1186/1758-2946-3-33},
  year = {2011},
  publisher = {Springer Science $\mathplus$ Business Media},
  volume = {3},
  number = {1},
  pages = {33},
  author = {Noel M O{\textquotesingle}Boyle and Michael Banck and Craig A James and Chris Morley and Tim Vandermeersch and Geoffrey R Hutchison},
  title = {{Open Babel: An open chemical toolbox}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/21982300}{21982300}] [PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3198950}{PMC3198950}] [doi:\href{http://dx.doi.org/10.1186/1758-2946-3-33}{10.1186/1758-2946-3-33}]},
  journal = {Journal of Cheminformatics},
}


@article{Wang_2000,
  doi = {10.1007/s0089400060498},
  url = {http://dx.doi.org/10.1007/s0089400060498},
  year = {2000},
  month = {Aug},
  publisher = {Springer Science $\mathplus$ Business Media},
  volume = {6},
  number = {7-8},
  pages = {498--516},
  author = {Renxiao Wang and Ying Gao and Luhua Lai},
  title = {{{LigBuilder}: A Multi-Purpose Program for Structure-Based Drug Design}},
  journal = {Journal of Molecular Modeling},
}


@article{Wolber_2005,
  doi = {10.1021/ci049885e},
  url = {http://dx.doi.org/10.1021/ci049885e},
  year = {2005},
  month = {jan},
  publisher = {American Chemical Society ({ACS})},
  volume = {45},
  number = {1},
  pages = {160--169},
  author = {Gerhard Wolber and Thierry Langer},
  title = {{{LigandScout}:~ 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters}},
  journal = {Journal of Chemical Information and Modeling},
}


@article{Schneidman_Duhovny_2008,
  doi = {10.1093/nar/gkn187},
  url = {http://dx.doi.org/10.1093/nar/gkn187},
  year = {2008},
  month = {may},
  publisher = {Oxford University Press ({OUP})},
  volume = {36},
  number = {Web Server},
  pages = {W223--W228},
  author = {D. Schneidman-Duhovny and O. Dror and Y. Inbar and R. Nussinov and H. J. Wolfson},
  title = {{{PharmaGist}: a webserver for ligand-based pharmacophore detection}},
  journal = {Nucleic Acids Research},
}


@article{Koes_2011,
  doi = {10.1021/ci200097m},
  url = {http://dx.doi.org/10.1021/ci200097m},
  year = {2011},
  month = {Jun},
  publisher = {American Chemical Society ({ACS})},
  volume = {51},
  number = {6},
  pages = {1307--1314},
  author = {David Ryan Koes and Carlos J. Camacho},
  title = {{Pharmer: Efficient and Exact Pharmacophore Search}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/21604800}{21604800}] [PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3124593}{PMC3124593}] [doi:\href{http://dx.doi.org/10.1021/ci200097m}{10.1021/ci200097m}]},
  journal = {Journal of Chemical Information and Modeling},
}


@article{Nicholls_2010,
  doi = {10.1021/jm900818s},
  url = {http://dx.doi.org/10.1021/jm900818s},
  year = {2010},
  month = {May},
  publisher = {American Chemical Society ({ACS})},
  volume = {53},
  number = {10},
  pages = {3862--3886},
  author = {Anthony Nicholls and Georgia B. McGaughey and Robert P. Sheridan and Andrew C. Good and Gregory Warren and Magali Mathieu and Steven W. Muchmore and Scott P. Brown and J. Andrew Grant and James A. Haigh and Neysa Nevins and Ajay N. Jain and Brian Kelley},
  title = {{Molecular Shape and Medicinal Chemistry: A Perspective}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/20158188}{20158188}] [PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874267}{PMC2874267}] [doi:\href{http://dx.doi.org/10.1021/jm900818s}{10.1021/jm900818s}]},
  journal = {J. Med. Chem.},
}


@article{Trott_2009,
  author = {Trott, Oleg and Olson, Arthur J.},
  title = {{AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading}},
  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/19499576}{19499576}] [PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041641}{PMC3041641}] [doi:\href{http://dx.doi.org/10.1002/jcc.21334}{10.1002/jcc.21334}]},
  journal = {Journal of Computational Chemistry},
  volume = {31},
  number = {2},
  publisher = {Wiley Subscription Services, Inc., A Wiley Company},
  issn = {1096-987X},
  url = {http://dx.doi.org/10.1002/jcc.21334},
  doi = {10.1002/jcc.21334},
  pages = {455--461},
  keywords = {AutoDock, molecular docking, virtual screening, computer-aided drug design, multithreading, scoring function},
  year = {2010},
}


@article{Hawkins_2007,
  doi = {10.1021/jm0603365},
  url = {http://dx.doi.org/10.1021/jm0603365},
  year = {2007},
  month = {jan},
  publisher = {American Chemical Society ({ACS})},
  volume = {50},
  number = {1},
  pages = {74--82},
  author = {Paul C. D. Hawkins and A. Geoffrey Skillman and Anthony Nicholls},
  title = {{Comparison of Shape-Matching and Docking as Virtual Screening Tools}},
  journal = {J. Med. Chem.},
}


@article{Labb__2015,
  doi = {10.1093/nar/gkv306},
  url = {http://dx.doi.org/10.1093/nar/gkv306},
  year = {2015},
  month = {apr},
  publisher = {Oxford University Press ({OUP})},
  volume = {43},
  number = {W1},
  pages = {W448--W454},
  author = {C{\'{e}}line M. Labb{\'{e}} and Julien Rey and David Lagorce and Marek Vavru{\v{s}}a and J{\'{e}}rome Becot and Olivier Sperandio and Bruno O. Villoutreix and Pierre Tuff{\'{e}}ry and Maria A. Miteva},
  title = {{{MTiOpenScreen}: a web server for structure-based virtual screening}},
  journal = {Nucleic Acids Res},
}


@article{Li_2014,
  doi = {10.1371/journal.pone.0085678},
  url = {http://dx.doi.org/10.1371/journal.pone.0085678},
  year = {2014},
  month = {jan},
  publisher = {Public Library of Science ({PLoS})},
  volume = {9},
  number = {1},
  pages = {e85678},
  author = {Hongjian Li and Kwong-Sak Leung and Pedro J. Ballester and Man-Hon Wong},
  editor = {Julio Vera},
  title = {{istar: A Web Platform for Large-Scale Protein-Ligand Docking}},
  journal = {{PLoS} {ONE}},
}


@article{Douguet_2010,
  doi = {10.1093/nar/gkq322},
  url = {http://dx.doi.org/10.1093/nar/gkq322},
  year = {2010},
  month = {may},
  publisher = {Oxford University Press ({OUP})},
  volume = {38},
  number = {Web Server},
  pages = {W615--W621},
  author = {D. Douguet},
  title = {{e-{LEA}3D: a computational-aided drug design web server}},
  journal = {Nucleic Acids Research},
}


@article{Mysinger_2012,
  doi = {10.1021/jm300687e},
  url = {http://dx.doi.org/10.1021/jm300687e},
  year = {2012},
  month = {jul},
  publisher = {American Chemical Society ({ACS})},
  volume = {55},
  number = {14},
  pages = {6582--6594},
  author = {Michael M. Mysinger and Michael Carchia and John. J. Irwin and Brian K. Shoichet},
  title = {{Directory of Useful Decoys Enhanced ({DUD}-E): Better Ligands and Decoys for Better Benchmarking}},
  journal = {J. Med. Chem.},
}
