deletions | additions       diff --git a/bibliography/biblio.bib b/bibliography/biblio.bib  index 75b9c1a..cd7609e 100644  --- a/bibliography/biblio.bib  +++ b/bibliography/biblio.bib 
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@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}, 
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@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}, 
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@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}, 
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@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}, 
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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},  } 
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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},  } 
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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},  } 
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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.},  } 
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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}},  } 
...
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},  } 
...
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}, 
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pages = {1607--1620},  author = {Marijn P. A. Sanders, Arménio J. M. Barbosa, Barbara Zarzycka, Gerry A.F. Nicolaes, Jan P.G. Klomp, Jacob de Vlieg, and Alberto Del Rio},  title = {{Comparative Analysis of Pharmacophore Screening Tools}},  note = {[PubMed:\http://www.ncbi.nlm.nih.gov/pubmed/22646988}{22646988}]  [doi:\href{http://dx.doi.org/10.1021/ci2005274}{10.1021/ci2005274}]}, {{[PubMed:\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}, 
...
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},  } 
...
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},  } 
...
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.},  } 
...
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},  } 
...
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},  } 
...
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},  } 
...
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}},  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/15667141}{15667141}] [doi:\href{http://dx.doi.org/10.1021/ci049885e}{10.1021/ci049885e}]}, journal = {Journal of Chemical Information and Modeling},  } 
...
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}},  note = {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/18424800}{18424800}] [PubMed Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447755}{PMC2447755}] [doi:\href{http://dx.doi.org/10.1093/nar/gkn187}{10.1093/nar/gkn187}]}, journal = {Nucleic Acids Research},  } 
...
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},  } 
...
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, @article{Trott_2009,  author = {Trott, Oleg and Olson, Arthur J.}, title = {AutoDock {{AutoDock  Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading}, 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.},  }