this is for holding javascript data
David Koes add links to bib
about 8 years ago
Commit id: 6a97134d7fe0df1b03b0368d5b55f3e6aea46088
deletions | additions
diff --git a/bibliography/biblio.bib b/bibliography/biblio.bib
index b70b7c2..04e18ba 100644
--- a/bibliography/biblio.bib
+++ b/bibliography/biblio.bib
...
@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},
...
@misc{moe,
title = {{Molecular Operating Environment (MOE)}},
author note =
{{Chemical Computing Group}},
year = {2016},
publisher = {Chemical Computing Group Inc. Montreal, QC},
}
@article{vams,
title = {{Shape-based virtual screening with volumetric aligned molecular shapes.}},
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.}},
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}},
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}}},
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}},
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}},
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 = {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}}},
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 and 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.},
}
@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}},
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?}},
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}},
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}},
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}},
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},
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},
} {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/19075767}{19075767}]
