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@article{Guha2006,
address = {Pennsylvania State University, University Park, Pennsylvania 16804-3000, Jmol Project, USA.},
author = {Guha, R. and Howard, M. T. and Hutchison, G. R. and Murray-Rust, P. and Rzepa, H. and Steinbeck, C. and Wegner, J. and Willighagen, E. L.},
day = {1},
NOdoi = {10.1021/ci050400b},
issn = {1549-9596},
journal = {J. Chem. Inf. Model.},
keywords = {blueobelisk, papers},
month = may,
number = {3},
pages = {991--998},
pmid = {16711717},
posted-at = {2007-01-14 11:31:40},
priority = {0},
publisher = {American Chemical Society},
title = {The Blue Obelisk - Interoperability in Chemical Informatics},
NOurl = {http://dx.doi.org/10.1021/ci050400b},
volume = {46},
year = {2006}
}
@article{Placzek2017,
author = {Placzek, Sandra and Schomburg, Ida and Chang, Antje and Jeske, Lisa and Ulbrich, Marcus and Tillack, Jana and Schomburg, Dietmar},
day = {04},
NOdoi = {10.1093/nar/gkw952},
issn = {0305-1048},
journal = {Nucleic Acids Research},
month = jan,
number = {D1},
pages = {D380--D388},
posted-at = {2017-05-07 13:24:36},
priority = {2},
title = {{BRENDA} in 2017: new perspectives and new tools in {BRENDA}},
NOurl = {http://dx.doi.org/10.1093/nar/gkw952},
volume = {45},
year = {2017}
}
@article{Weininger1988,
author = {Weininger, David},
issn = {0095-2338},
journal = {J. Chem. Inf. Comput. Sci.},
keywords = {smiles},
month = feb,
number = {1},
pages = {31--36},
posted-at = {2004-11-29 21:24:58},
publisher = {American Chemical Society},
title = {{SMILES}, a chemical language and information system. 1. introduction to methodology and encoding rules},
volume = {28},
year = {1988}
}
@article{Guha2006,
abstract = {We present an overview of the nightly build system for the {CDK} distribution},
author = {Guha, R.},
issn = {1614-7553},
journal = {CDK News},
keywords = {dev},
month = sep,
number = {2},
pages = {32--34},
posted-at = {2015-05-15 21:11:01},
priority = {2},
title = {The {CDK} Nightly Build System},
NOurl = {https://sourceforge.net/projects/cdk/files/CDK\%20News/3\_2/},
volume = {3},
year = {2006}
}
@book{GroovyCDK,
author = {Willighagen, E. L.},
NOdoi = {10.6084/m9.figshare.2057790.v1},
edition = {{1.4.1-0}},
publisher = {Figshare},
keywords = {cdk, cheminformatics, java},
posted-at = {2015-12-23 16:31:39},
priority = {2},
title = {Groovy Cheminformatics with the Chemistry Development Kit},
url = {https://doi.org/10.6084/m9.figshare.2057790.v1},
year = {2011}
}
@misc{Segler2016,
author = {Segler, Marwin H. S. and Waller, Mark P.},
citeulike-article-id = {14320138},
citeulike-linkout-0 = {http://dx.doi.org/10.1002/chem.201604556},
NOdoi = {10.1002/chem.201604556},
issn = {09476539},
journal = {Chemistry - A European Journal},
month = jan,
posted-at = {2017-03-26 11:00:19},
priority = {2},
title = {Modelling Chemical Reasoning to Predict and Invent Reactions},
NOurl = {https://doi.org/10.1002/chem.201604556},
year = {2017}
}
@article{Hanson2010,
abstract = {Recent advances in molecular and crystallographic visualization methods are allowing instructors unprecedented opportunities to enhance student learning using virtual models within a familiar web-browser context. In step with these advances, the latest versions of the Jmol molecular visualization applet offer capabilities that hold potential for revolutionizing the way students learn about symmetry, uncertainty and the overall enterprise of molecular structure determination.},
author = {Hanson, Robert M.},
citeulike-article-id = {7757032},
citeulike-linkout-0 = {http://dx.doi.org/10.1107/s0021889810030256},
citeulike-linkout-1 = {http://scripts.iucr.org/cgi-bin/paper?S0021889810030256},
day = {01},
NOdoi = {10.1107/s0021889810030256},
issn = {0021-8898},
journal = {Journal of Applied Crystallography},
keywords = {cheminformatics, jmol, opensource},
month = oct,
pages = {1250--1260},
posted-at = {2010-09-02 20:23:55},
priority = {5},
publisher = {International Union of Crystallography},
title = {Jmol - a paradigm shift in crystallographic visualization},
NOurl = {http://dx.doi.org/10.1107/s0021889810030256},
volume = {43},
year = {2010}
}
@article{Willighagen2007jmol,
author = {Willighagen, Egon and Howard, Miguel},
citeulike-article-id = {6483686},
citeulike-linkout-0 = {http://dx.doi.org/10.1038/npre.2007.50.1},
citeulike-linkout-1 = {http://precedings.nature.com/documents/50/version/1},
day = {14},
NOdoi = {10.1038/npre.2007.50.1},
issn = {9999-9999},
journal = {Nature Precedings},
keywords = {applet, bioinformatics, cheminformatics, chemistry, free\_open\_source, java, java\_applications, jmol, molecular\_graphics, papers, preprint, visualization, web},
month = jun,
number = {713},
posted-at = {2016-09-18 20:01:41},
priority = {2},
publisher = {Nature Publishing Group},
title = {Fast and Scriptable Molecular Graphics in Web Browsers without {Java3D}},
NOurl = {http://dx.doi.org/10.1038/npre.2007.50.1},
year = {2007}
}
@article{krause2000jchempaint,
title={{JChemPaint} - using the collaborative forces of the internet to develop a free editor for {2D} chemical structures},
author={Krause, Stefan and Willighagen, Egon and Steinbeck, Christoph},
journal={Molecules},
volume={5},
number={1},
pages={93--98},
year={2000},
publisher={Molecular Diversity Preservation International}
}
@article{Carlsson2010,
author = {Carlsson, Lars and Spjuth, Ola and Adams, Samuel and Glen, Robert C. and Boyer, Scott},
NOdoi = {10.1186/1471-2105-11-362},
issn = {1471-2105},
journal = {BMC Bioinformatics},
keywords = {bioclipse, cdk, cheminformatics, metabolism},
number = {1},
pages = {362+},
pmid = {20594327},
posted-at = {2010-07-05 16:29:31},
priority = {2},
title = {Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using {MetaPrint2D} and Bioclipse},
NOurl = {http://dx.doi.org/10.1186/1471-2105-11-362},
volume = {11},
year = {2010}
}
@article{Rostkowski2013,
author = {Rostkowski, Micha{\l} and Spjuth, Ola and Rydberg, Patrik},
day = {15},
NOdoi = {10.1093/bioinformatics/btt325},
issn = {1460-2059},
journal = {Bioinformatics},
month = aug,
number = {16},
pages = {2051--2052},
pmid = {23740742},
posted-at = {2013-06-11 05:33:24},
priority = {2},
publisher = {Oxford University Press},
title = {{WhichCyp}: prediction of cytochromes P450 inhibition},
NOurl = {http://dx.doi.org/10.1093/bioinformatics/btt325},
volume = {29},
year = {2013}
}
@article{Gushurst91,
author = {Alan J. Gushurst and James G. Nourse and W. Douglas Hounshell and Burton A. Leland and David G. Raich},
title = {The substance module: the representation, storage, and searching of complex structures},
journal = {Journal of Chemical Information and Computer Sciences},
volume = {31},
number = {4},
pages = {447-454},
year = {1991},
NOdoi = {10.1021/ci00004a003},
NOURL = {
http://dx.doi.org/10.1021/ci00004a003
},
NOeprint = {
http://dx.doi.org/10.1021/ci00004a003
}
}
@misc{rdkit,
title = {{RDKit: Open-Source Cheminformatics Software}},
howpublished = {\url{http://www.rdkit.org}},
key = {RDKit, online}
}
@article{OBoyle2011,
author="O'Boyle, Noel M.
and Banck, Michael
and James, Craig A.
and Morley, Chris
and Vandermeersch, Tim
and Hutchison, Geoffrey R.",
title="{Open Babel}: An open chemical toolbox",
journal="Journal of Cheminformatics",
year="2011",
volume="3",
number="1",
pages="1--14",
abstract="A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats.",
issn="1758-2946",
NOdoi="10.1186/1758-2946-3-33",
NOurl="http://dx.doi.org/10.1186/1758-2946-3-33"
}
@article{Dalby92,
author = {Arthur Dalby and James G. Nourse and W. Douglas Hounshell and Ann K. I. Gushurst and David L. Grier and Burton A. Leland and John Laufer},
title = {Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited},
journal = {Journal of Chemical Information and Computer Sciences},
volume = {32},
number = {3},
pages = {244-255},
year = {1992},
NOdoi = {10.1021/ci00007a012},
NOURL = {
http://dx.doi.org/10.1021/ci00007a012
},
NOeprint = {
http://dx.doi.org/10.1021/ci00007a012
}
}
@article{ReactPRED,
author = {Sivakumar, Tadi V. and Giri, Varun and Park, Jin H. and Kim, Tae Y. and Bhaduri, Anirban},
day = {02},
NOdoi = {10.1093/bioinformatics/btw491},
issn = {1460-2059},
journal = {Bioinformatics},
month = aug,
pages = {btw491+},
pmid = {27485447},
posted-at = {2016-08-11 16:33:44},
priority = {2},
publisher = {Oxford University Press},
title = {{ReactPRED}: a tool to predict and analyze biochemical reactions},
NOurl = {http://dx.doi.org/10.1093/bioinformatics/btw491},
year = {2016}
}
@misc{ctfilespec,
url = {http://accelrys.com/products/collaborative-science/biovia-draw/ctfile-no-fee.html},
title = "CTfile Formats"}
@misc{ChemViz2,
url = {http://www.rbvi.ucsf.edu/cytoscape/chemViz2/},
title = "ChemViz2: Cheminformatics App for Cytoscape",
year = 2016
}
@article{Lawson2012,
author = {Lawson, Kevin R. and Lawson, Jonty},
day = {2},
NOdoi = {10.1186/1758-2946-4-3},
issn = {1758-2946},
journal = {Journal of Cheminformatics},
keywords = {cdk--usespackage--fingerprint, cdk--usespackage--isomorphism, cdk--usespackage--qsar, cdk--usespackage--renderer, cdk--usespackage--smiles},
month = feb,
number = {1},
pages = {3+},
pmcid = {PMC3310842},
pmid = {22301088},
posted-at = {2012-02-09 00:30:03},
priority = {2},
title = {{LICSS} - a chemical spreadsheet in microsoft excel},
NOurl = {http://dx.doi.org/10.1186/1758-2946-4-3},
volume = {4},
year = {2012}
}
@article{Berger2004,
author = {Berger, F. and Flamm, C. and Gleiss, P. M. and Leydold, J. and Stadler, P. F.},
NOdoi = {10.1021/ci030405d},
journal = {Journal of Chemical Information and Computer Sciences},
number = {2},
posted-at = {2010-09-23 07:38:56},
priority = {3},
title = {Counterexamples in chemical ring perception},
NOurl = {http://dx.doi.org/10.1021/ci030405d},
volume = {44},
year = {2004}
}
@article{Figueras1996,
address = {399 Baker's Pond Road, Orleans, Massachusetts 02653},
author = {Figueras, John},
day = {1},
NOdoi = {10.1021/ci960013p},
journal = {Journal of Chemical Information and Computer Sciences},
month = jan,
number = {5},
pages = {986--991},
posted-at = {2013-07-29 21:39:33},
priority = {2},
publisher = {American Chemical Society},
title = {Ring Perception Using {Breadth-First} Search},
NOurl = {http://dx.doi.org/10.1021/ci960013p},
volume = {36},
year = {1996}
}
@misc{Beam,
author = {May, John W},
url = {https://github.com/johnmay/beam},
title = "Beam",
publisher = "GitHub",
year = 2013
}
@article{Guha2007,
author = {Guha, Rajarshi},
issn = {1548-7660},
journal = {Journal of Statistical Software},
keywords = {r\_package, rcdk},
month = jan,
number = {5},
pages = {1--16},
posted-at = {2013-06-14 11:58:51},
priority = {2},
title = {Chemical Informatics Functionality in {R}},
NOurl = {http://www.jstatsoft.org/v18/i05},
volume = {18},
year = {2007}
}
@article{Karapetyan2015,
author = {Karapetyan, Karen and Batchelor, Colin and Sharpe, David and Tkachenko, Valery and Williams, Antony},
title = {The {Chemical Validation and Standardization Platform (CVSP)}: large-scale automated validation of chemical structure datasets},
journal = {Journal of Statistical Software},
year = {2015},
month = oct,
day = {28},
priority = {2},
NOurl = {https://jcheminf.springeropen.com/articles/10.1186/s13321-015-0072-8},
volume = {7},
number = {30}
}
@misc{AUTHORS,
title = {AUTHORS},
url = {https://github.com/cdk/cdk/blob/master/pom.xml},
year = {2015}
}
@article{RojasCherto2011,
abstract = {Motivation: Identification of metabolites is essential for its use as biomarkers, for research in systems biology and for drug discovery. The first step before a structure can be elucidated is to determine its elemental composition. High-resolution mass spectrometry, which provides the exact mass, together with common constraint rules, for rejecting false proposed elemental compositions, cannot always provide one unique elemental composition solution.},
author = {Rojas-Chert\'{o}, Miguel and Kasper, Piotr T. and Willighagen, Egon L. and Vreeken, Rob J. and Hankemeier, Thomas and Reijmers, Theo H.},
day = {01},
issn = {1460-2059},
journal = {Bioinformatics},
keywords = {cdk--usespackage--formula, metabolomics},
month = sep,
number = {17},
pages = {2376--2383},
pmid = {21757467},
posted-at = {2011-07-15 11:06:46},
priority = {2},
publisher = {Oxford University Press},
title = {Elemental composition determination based on {MSn}},
NOurl = {http://dx.doi.org/10.1093/bioinformatics/btr409},
volume = {27},
year = {2011}
}
@article{May2014,
author = {May, John W. and Steinbeck, Christoph},
day = {30},
issn = {1758-2946},
journal = {{Journal of Cheminformatics}},
month = jan,
number = {1},
pages = {3+},
pmid = {24479757},
posted-at = {2014-01-30 14:49:36},
priority = {2},
publisher = {Chemistry Central Ltd},
title = {Efficient ring perception for the {Chemistry Development Kit}},
NOurl = {http://dx.doi.org/10.1186/1758-2946-6-3},
volume = {6},
year = {2014}
}
@misc{May2014_SMARTS,
author = {May, John W.},
day = {26},
month = mar,
title = {Mischievous SMARTS Queries},
url = {http://efficientbits.blogspot.co.uk/2014_03_01_archive.html},
year = {2014}
}
@misc{May2015,
author = {May, John W.},
day = {6},
month = jan,
publisher = {University of Cambridge},
title = {Cheminformatics for genome-scale metabolic reconstructions},
url = {https://www.repository.cam.ac.uk/handle/1810/246652},
year = {2015}
}
@misc{MayBlog2013a,
author = {May, John W.},
title = {All the small things},
howpublished = {http://efficientbits.blogspot.co.uk/2013/10/all-small-things.html},
year = {2013},
day = {25},
month = oct
}
@misc{MayBlog2013b,
author = {May, John W.},
title = {Improved substructure matching},
howpublished = {http://efficientbits.blogspot.co.uk/2013/11/improved-substructure-matching.html},
year = {2013},
day = {11},
month = nov
}
@Article{Clark2014,
AUTHOR = {Clark, Alex and Sarker, Malabika and Ekins, Sean},
TITLE = {New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0},
JOURNAL = {Journal of Cheminformatics},
VOLUME = {6},
YEAR = {2014},
NUMBER = {1},
PAGES = {38},
NOURL = {http://www.jcheminf.com/content/6/1/38},
NODOI = {10.1186/s13321-014-0038-2},
PubMedID = {},
ISSN = {1758-2946}
}
@article{signaturefingerprints,
author = {Alvarsson, Jonathan and Eklund, Martin and Engkvist, Ola and Spjuth, Ola and Carlsson, Lars and Wikberg, Jarl E. S. and Noeske, Tobias},
title = {Ligand-Based Target Prediction with Signature Fingerprints},
journal = {Journal of Chemical Information and Modeling},
volume = {54},
number = {10},
pages = {2647-2653},
year = {2014},
}
@article{Spjuth2013,
author = {Spjuth, Ola and Berg, Arvid and Adams, Samuel and Willighagen, Egon L.},
day = {13},
issn = {1758-2946},
journal = {Journal of Cheminformatics},
keywords = {cdk--useslibrary},
month = mar,
number = {1},
pages = {14+},
pmid = {23497723},
posted-at = {2013-03-13 11:03:52},
priority = {2},
publisher = {Chemistry Central Ltd},
title = {Applications of the {InChI} in cheminformatics with the {CDK} and Bioclipse},
NOurl = {http://dx.doi.org/10.1186/1758-2946-5-14},
volume = {5},
year = {2013}
}
@article{OBoyle2011b,
author = {O'Boyle, Noel and Guha, Rajarshi and Willighagen, Egon and Adams, Samuel and Alvarsson, Jonathan and Bradley, Jean C. and Filippov, Igor and Hanson, Robert and Hanwell, Marcus and Hutchison, Geoffrey and James, Craig and Jeliazkova, Nina and Lang, Andrew and Langner, Karol and Lonie, David and Lowe, Daniel and Pansanel, Jerome and Pavlov, Dmitry and Spjuth, Ola and Steinbeck, Christoph and Tenderholt, Adam and Theisen, Kevin and Murray-Rust, Peter},
issn = {1758-2946},
journal = {{Journal of Cheminformatics}},
number = {1},
pages = {37+},
pmcid = {PMC3205042},
pmid = {21999342},
posted-at = {2011-10-14 16:51:29},
priority = {2},
title = {{Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on}},
NOurl = {http://www.jcheminf.com/content/3/1/37},
volume = {3},
year = {2011}
}
@article{Steinbeck2003,
address = {Max-Planck-Institute of Chemical Ecology, Jena, Germany. [email protected]},
author = {Steinbeck, C. and Han, Y. and Kuhn, S. and Horlacher, O. and Luttmann, E. and Willighagen, E.},
issn = {0095-2338},
journal = {J Chem Inf Comput Sci},
keywords = {cheminformatics, java, opensource, papers},
number = {2},
pages = {493--500},
posted-at = {2007-06-09 09:31:09},
priority = {0},
title = {{The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics.}},
NOurl = {http://dx.doi.org/10.1021/ci025584y},
volume = {43},
year = {2003}
}
@article{Klekota2008,
author = {Klekota, Justin and Roth, Frederick P},
file = {:Users/jonathan/Library/Application Support/Mendeley Desktop/Downloaded/Klekota, Roth - 2008 - Chemical substructures that enrich for biological activity.pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics},
keywords = {Animals,Cells, Cultured,Combinatorial Chemistry Techniques,Databases, Factual,Drug Design,Humans,Ligands,Pharmaceutical Preparations,Pharmaceutical Preparations: chemistry,Structure-Activity Relationship},
month = nov,
number = {21},
pages = {2518--25},
pmid = {18784118},
title = {{Chemical substructures that enrich for biological activity.}},
NOurl = {http://bioinformatics.oxfordjournals.org/content/24/21/2518.short},
volume = {24},
year = {2008}
}
@article{Hall1995,
abstract = {The electrotopological state formalism is developed further in conjunction with atom classification. The classification scheme is based on the characteristics of hydride groups: (1) atomic number of an atom as element identifier, (2) a valence state designation consisting of valence and simple connectivity 6 values (for each atom together with its bonded hydrogen atoms, as in -CH3 or -NH-), and (3) an aromaticity indicator. This scheme may be viewed as a three-dimensional array. In a few cases, bonded neighbor analysis is also required. The scheme is developed and illustrated. For each atom type in a molecule, the electrotopological state indices are summed. These atom type E-state indices, based on a summation of E-state values, are useful for database characterization, molecular similarity analysis, and QSAR. A QSAlU QSPR example is given for boiling point for a set of 245 alkanes and alcohols for which the standard error is 8.0 "C},
author = {Hall, Lowell H and Kier, Lemont B},
issn = {15499596},
journal = {Journal of Chemical Information and Modeling},
pages = {1039--1045},
title = {{Electrotopological State Indices for Atom Types: A Novel Combination of Electronic, Topological, and Valence State Information}},
volume = {35},
year = {1995}
}
@article{Steinbeck2006,
address = {Cologne University Bioinformatics Center (CUBIC), Germany. [email protected]},
author = {Steinbeck, C. and Hoppe, C. and Kuhn, S. and Floris, M. and Guha, R. and Willighagen, E. L.},
issn = {1381-6128},
journal = {{Current Pharmaceutical Design}},
keywords = {cheminformatics, java, opensource, papers},
number = {17},
pages = {2111--2120},
posted-at = {2007-06-09 09:28:49},
priority = {0},
title = {{Recent developments of the Chemistry Development Kit (CDK) - an open-source java library for chemo- and bioinformatics.}},
NOurl = {http://dx.doi.org/10.2174/138161206777585274},
volume = {12},
year = {2006}
}
@article{OBoyle2008,
author = {O'Boyle, N. M. and Hutchison, G. R.},
issn = {1752-153X},
journal = {Chemistry Central Journal},
keywords = {cheminformatics, python},
posted-at = {2009-04-06 08:47:48},
priority = {2},
title = {Cinfony - combining Open Source cheminformatics toolkits behind a common interface.},
NOurl = {http://dx.doi.org/10.1186/1752-153X-2-24},
volume = {2},
year = {2008}
}
@article{Beisken2013,
author = {Beisken, Stephan and Meinl, Thorsten and Wiswedel, Bernd and de Figueiredo, Luis and Berthold, Michael and Steinbeck, Christoph},
day = {22},
issn = {1471-2105},
journal = {BMC Bioinformatics},
keywords = {cdk--useslibrary},
month = aug,
number = {1},
pages = {257+},
posted-at = {2013-08-27 07:46:29},
priority = {2},
title = {{KNIME}-{CDK}: Workflow-driven cheminformatics},
volume = {14},
year = {2013}
}
@article{Truszkowski2011,
title={{New developments on the cheminformatics open workflow environment CDK-Taverna}},
author={Truszkowski, Andreas and Jayaseelan, Kalai Vanii and Neumann, Stefan and Willighagen, Egon L and Zielesny, Achim and Steinbeck, Christoph},
journal={{Journal of Cheminformatics}},
volume={3},
number={1},
pages={1--10},
year={2011},
publisher={Springer}
}
@article{Peironcely2012,
title={{OMG: open molecule generator}},
author={Peironcely, Julio E and Rojas-Chert{\'o}, Miguel and Fichera, Davide and Reijmers, Theo and Coulier, Leon and Faulon, Jean-Loup and Hankemeier, Thomas},
journal={{Journal of Cheminformatics}},
volume={4},
number={1},
pages={1--13},
year={2012},
publisher={Springer}
}
@article{yap2011padel,
title={{PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints}},
author={Yap, Chun Wei},
journal={{Journal of Computational Chemistry}},
volume={32},
number={7},
pages={1466--1474},
year={2011},
publisher={Wiley Online Library}
}
@article{jeliazkova2011ambit,
title={{AMBIT RESTful web services: an implementation of the OpenTox application programming interface}},
author={Jeliazkova, Nina and Jeliazkov, Vedrin},
journal={{Journal of Cheminformatics}},
volume={3},
number={1},
pages={1--18},
year={2011},
publisher={Springer}
}
@article{jeliazkova2011ambitsmarts,
title={{AMBIT-SMARTS: Efficient Searching of Chemical Structures and Fragments}},
author={Jeliazkova, Nina and Kochev, Nikolay},
journal={Molecular Informatics},
volume={30},
number={8},
pages={707--720},
year={2011},
publisher={Wiley Online Library}
}
@article{kochev2013ambit,
title={Ambit-Tautomer: An Open Source Tool for Tautomer Generation},
author={Kochev, Nikolay T and Paskaleva, Vesselina H and Jeliazkova, Nina},
journal={Molecular Informatics},
volume={32},
number={5-6},
pages={481--504},
year={2013},
publisher={Wiley Online Library}
}
@article{Hinselmann2011,
author = {Hinselmann, Georg and Rosenbaum, Lars and Jahn, Andreas and Fechner, Nikolas and Zell, Andreas},
issn = {1758-2946},
journal = {Journal of Cheminformatics},
keywords = {cdk, cheminformatics, fingerprint},
number = {1},
pages = {3+},
pmid = {21219648},
posted-at = {2011-01-10 20:10:26},
priority = {2},
title = {{jCompoundMapper}: An open source Java library and command-line tool for chemical fingerprints},
volume = {3},
year = {2011}
}
@article{wetzel2009interactive,
title={Interactive exploration of chemical space with {Scaffold Hunter}},
author={Wetzel, Stefan and Klein, Karsten and Renner, Steffen and Rauh, Daniel and Oprea, Tudor I and Mutzel, Petra and Waldmann, Herbert},
journal={Nature Chemical Biology},
volume={5},
number={8},
pages={581--583},
year={2009},
publisher={Nature Publishing Group}
}
@article{spjuth2007bioclipse,
title={Bioclipse: an open source workbench for chemo-and bioinformatics},
author={Spjuth, Ola and Helmus, Tobias and Willighagen, Egon L and Kuhn, Stefan and Eklund, Martin and Wagener, Johannes and Murray-Rust, Peter and Steinbeck, Christoph and Wikberg, Jarl ES},
journal={{BMC Bioinformatics}},
volume={8},
number={1},
pages={59},
year={2007},
publisher={BioMed Central Ltd}
}
@article{spjuth2009bioclipse,
title={Bioclipse 2: A scriptable integration platform for the life sciences},
author={Spjuth, Ola and Alvarsson, Jonathan and Berg, Arvid and Eklund, Martin and Kuhn, Stefan and M{\"a}sak, Carl and Torrance, Gilleain and Wagener, Johannes and Willighagen, Egon L and Steinbeck, Christoph and others},
journal={{BMC Bioinformatics}},
volume={10},
number={1},
pages={397},
year={2009},
publisher={BioMed Central Ltd}
}
@article{rogers2010extended,
title={Extended-connectivity fingerprints},
author={Rogers, David and Hahn, Mathew},
journal={{Journal of Chemical Information and Modeling}},
volume={50},
number={5},
pages={742--754},
year={2010},
publisher={ACS Publications}
}
@article{vidal2005lingo,
title={LINGO, an efficient holographic text based method to calculate biophysical properties and intermolecular similarities},
author={Vidal, David and Thormann, Michael and Pons, Miquel},
journal={{Journal of Chemical Information and Modeling}},
volume={45},
number={2},
pages={386--393},
year={2005},
publisher={ACS Publications}
}
@misc{pubchemFP,
Lastchecked = {Friday 4 July 2014},
Title = {{PubChem Substructure Fingerprint v1.3}},
Url = {ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.txt}
}
@article{Rahman2014,
author = {Rahman, Syed A. and Cuesta, Sergio M. and Furnham, Nicholas and Holliday, Gemma L. and Thornton, Janet M.},
day = {12},
issn = {1548-7091},
journal = {Nature Methods},
month = feb,
number = {2},
pages = {171--174},
posted-at = {2015-12-24 11:30:51},
priority = {2},
publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
title = {{EC}-{BLAST}: a tool to automatically search and compare enzyme reactions},
NOurl = {http://dx.doi.org/10.1038/nmeth.2803},
volume = {11},
year = {2014}
}
@article{Rahman2009,
author = {Rahman, Syed A. and Bashton, Matthew and Holliday, Gemma L. and Schrader, Rainer and Thornton, Janet M.},
day = {10},
issn = {1758-2946},
journal = {Journal of Cheminformatics},
keywords = {uucjc},
month = aug,
number = {1},
pages = {12+},
pmcid = {PMC2820491},
pmid = {20298518},
posted-at = {2010-02-05 11:59:18},
priority = {5},
publisher = {Chemistry Central Ltd},
title = {Small Molecule Subgraph Detector ({SMSD}) toolkit},
NOurl = {http://dx.doi.org/10.1186/1758-2946-1-12},
volume = {1},
year = {2009}
}
@incollection{Cannon2006,
author = {Cannon, Edward and Mitchell, John B. O.},
booktitle = {Computational Life Sciences II},
editor = {Berthold and Glen, RobertC and Fischer, Ingrid},
journal = {{Computational Life Sciences II}},
keywords = {cdk, fingerprint},
pages = {173--182},
posted-at = {2010-10-05 10:34:41},
priority = {2},
publisher = {Springer Berlin Heidelberg},
series = {Lecture Notes in Computer Science},
title = {Classifying the World {Anti-Doping} Agency's 2005 Prohibited List Using the {Chemistry Development Kit} Fingerprint},
address = {Heidelberg, Germany},
volume = {4216},
year = {2006}
}
@article{Marth2015,
author = {Marth, C. J. and Gallego, G. M. and Lee, J. C. and Lebold, T. P. and Kulyk, S. and Kou, K. G. M. and Qin, J. and Lilien, R. and Sarpong, R.},
day = {24},
issn = {0028-0836},
journal = {Nature},
keywords = {cdk--useslibrary},
month = dec,
number = {7583},
pages = {493--498},
posted-at = {2015-12-22 17:06:52},
priority = {2},
publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
title = {Network-analysis-guided synthesis of weisaconitine D and liljestrandinine},
NOurl = {http://dx.doi.org/10.1038/nature16440},
volume = {528},
year = {2015}
}
@article{Murray-Rust2011,
author = {Murray-Rust, Peter and Rzepa, Henry S.},
day = {14},
issn = {1758-2946},
journal = {{Journal of Cheminformatics}},
month = oct,
number = {1},
pages = {44+},
pmid = {21999549},
posted-at = {2014-03-22 17:24:21},
priority = {2},
publisher = {Chemistry Central Ltd},
title = {{CML}: Evolution and design},
NOurl = {http://dx.doi.org/10.1186/1758-2946-3-44},
volume = {3},
year = {2011}
}
@misc{Hicklin2012,
abstract = {{JAMA} is a basic linear algebra package for Java. It provides user-level classes for constructing and manipulating real, dense matrices. It is meant to provide sufficient functionality for routine problems, packaged in a way that is natural and understandable to non-experts. It is intended to serve as the standard matrix class for Java, and will be proposed as such to the Java Grande Forum and then to Sun. A straightforward public-domain reference implementation has been developed by the {MathWorks} and {NIST} as a strawman for such a class. We are releasing this version in order to obtain public comment. There is no guarantee that future versions of {JAMA} will be compatible with this one.},
author = {Hicklin, Joe and Moler, Cleve and Webb, Peter and Boisvert, Ronald F. and Miller, Bruce and Pozo, Roldan and Remington, Karin},
citeulike-article-id = {13894362},
day = {9},
edition = {1.0.3},
keywords = {java, matrix, nist},
month = nov,
posted-at = {2015-12-26 12:02:19},
priority = {2},
title = {{JAMA}: A Java Matrix Package},
url = {http://math.nist.gov/javanumerics/jama/},
year = {2012}
}
@article{Faulon2004,
author = {Faulon, Jean-Loup and Collins, Michael J. and Carr, Robert D.},
day = {10},
journal = {Journal of Chemical Information and Computer Sciences},
number = {2},
pages = {427-436},
title = {The Signature Molecular Descriptor. 4. Canonizing Molecules Using Extended Valence Sequences},
NOurl = {http://dx.doi.org/10.1021/ci0341823},
volume = {44},
year = {2004}
}
@article{Faulon2003,
author = {Faulon, Jean-Loup and Visco, Donald P., Jr. and Pophale, Ramdas S.},
day = {26},
journal = {Journal of Chemical Information and Computer Sciences},
number = {3},
pages = {707-720},
title = {The Signature Molecular Descriptor. 1. Using Extended Valence Sequences in {QSAR} and {QSPR} Studies},
NOurl = { http://dx.doi.org/10.1021/ci020345w},
volume = {43},
year = {2003}
}
@article{Pluskal2012,
author={Pluskal, Tomáš and Uehara, Taisuke and Yanagida, Mitsuhiro},
journal={Analytical Chemistry},
volume={84},
number={10},
title={Highly accurate chemical formula prediction tool utilizing high-resolution mass spectra, {MS/MS} fragmentation, heuristic rules, and isotope pattern matching},
pages={4396-4403},
year={2012},
publisher={ACS Publications},
NOdoi = {10.1021/ac3000418},
NOurl = {http://dx.doi.org/10.1021/ac3000418}}
@article{Spjuth2011DS,
Author = {Spjuth, Ola and Eklund, Martin and Ahlberg Helgee, Ernst and Boyer, Scott and Carlsson, Lars},
Date-Added = {2016-08-08 13:39:50 +0000},
Date-Modified = {2016-08-08 13:39:50 +0000},
NODoi = {10.1021/ci200242c},
Journal = { Journal of Chemical Information and Modeling },
Journal-Full = {Journal of chemical information and modeling},
Mesh = {Algorithms; Carcinogens; Chemistry, Pharmaceutical; Computer Simulation; Data Mining; Databases, Factual; Drug Design; Drug Discovery; Drug-Related Side Effects and Adverse Reactions; Humans; Models, Chemical; Molecular Structure; Mutagens; Pharmaceutical Preparations; Position-Specific Scoring Matrices; Quantitative Structure-Activity Relationship; Receptors, Aryl Hydrocarbon; Software},
Month = {Aug},
Number = {8},
Pages = {1840-7},
Pmid = {21774475},
Pst = {ppublish},
Title = {Integrated decision support for assessing chemical liabilities},
Volume = {51},
Year = {2011},
Bdsk-Url-1 = {http://dx.doi.org/10.1021/ci200242c}}
@article{Moghadam2015,
Author = {Moghadam, Behrooz Torabi and Alvarsson, Jonathan and Holm, Marcus and Eklund, Martin and Carlsson, Lars and Spjuth, Ola},
Date-Added = {2016-08-08 13:41:40 +0000},
Date-Modified = {2016-08-08 13:41:40 +0000},
NODoi = {10.1021/ci500580y},
Journal = { Journal of Chemical Information and Modeling },
Journal-Full = {Journal of chemical information and modeling},
Mesh = {Computational Biology; Computing Methodologies; Databases, Chemical; Databases, Factual; Drug Discovery; Internet; Ligands; Quantitative Structure-Activity Relationship; Software},
Month = {Jan},
Number = {1},
Pages = {19-25},
Pmid = {25493610},
Pst = {ppublish},
Title = {Scaling predictive modeling in drug development with cloud computing},
Volume = {55},
Year = {2015},
Bdsk-Url-1 = {http://dx.doi.org/10.1021/ci500580y}}
@article{Alvarsson2014,
Author = {Alvarsson, Jonathan and Eklund, Martin and Andersson, Claes and Carlsson, Lars and Spjuth, Ola and Wikberg, Jarl E S},
Date-Added = {2016-08-08 13:41:40 +0000},
Date-Modified = {2016-08-08 13:41:40 +0000},
NODoi = {10.1021/ci500344v},
Journal = { Journal of Chemical Information and Modeling },
Journal-Full = {Journal of chemical information and modeling},
Mesh = {Benchmarking; Drug Evaluation, Preclinical; Quantitative Structure-Activity Relationship; Support Vector Machine},
Month = {Nov},
Number = {11},
Pages = {3211-7},
Pmid = {25318024},
Pst = {ppublish},
Title = {Benchmarking study of parameter variation when using signature fingerprints together with support vector machines},
Volume = {54},
Year = {2014},
Bdsk-Url-1 = {http://dx.doi.org/10.1021/ci500344v}}
@article{Spjuth2012OS,
Author = {Spjuth, Ola and Carlsson, Lars and Alvarsson, Jonathan and Georgiev, Valentin and Willighagen, Egon and Eklund, Martin},
Date-Added = {2016-08-08 13:41:40 +0000},
Date-Modified = {2016-08-08 13:41:40 +0000},
Journal = {Current Topics in Medicinal Chemistry},
Journal-Full = {Current topics in medicinal chemistry},
Mesh = {Absorption; Algorithms; Decision Support Techniques; Drug Discovery; Drug Evaluation, Preclinical; Pharmacokinetics; Software; Toxicology},
Number = {18},
Pages = {1980-6},
Pmid = {23110533},
Pst = {ppublish},
Title = {Open source drug discovery with {Bioclipse}},
Volume = {12},
Year = {2012}}
@article{Norinder2013,
Abstract = {A quantitative structure-activity relationship investigation of some NaV1.7 active compounds has been performed by repeated, random, external test set experiments employing structural descriptors (fingerprints) of signature type in combination with support vector machine (SVM) analysis using the radial basis function (RBF) kernel. The results from the investigation show remarkably stable performance from the derived in silico models in terms of statistical measures such as correlation coefficients as well as root mean squared errors (RMSEs) for the randomly selected external test sets. Also, the Bioclipse Modeling platform is utilized for introducing interpretation to the derived models.},
Author = {Norinder, Ulf and Ek, Maria E},
Date-Added = {2016-08-08 13:43:47 +0000},
Date-Modified = {2016-08-08 13:43:47 +0000},
NODoi = {10.1016/j.bmcl.2012.10.102},
Journal = {Bioorg Med Chem Lett},
Journal-Full = {Bioorganic \& medicinal chemistry letters},
Mesh = {Models, Molecular; NAV1.7 Voltage-Gated Sodium Channel; Quantitative Structure-Activity Relationship; Support Vector Machine},
Month = {Jan},
Number = {1},
Pages = {261-3},
Pmid = {23177785},
Pst = {ppublish},
Title = {{QSAR} investigation of {NaV1.7} active compounds using the {SVM}/Signature approach and the {Bioclipse} Modeling platform},
Volume = {23},
Year = {2013},
Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.bmcl.2012.10.102}}
@inproceedings{Duehrkop2013,
title={Faster mass decomposition},
author={D{\"u}hrkop, Kai and Ludwig, Marcus and Meusel, Marvin and B{\"o}cker, Sebastian},
booktitle={Proc. of Workshop on Algorithms in Bioinformatics (WABI 2013)},
pages={45-58},
year={2013},
organization={Springer},
url={http://arxiv.org/abs/1307.7805}}
@article{Boecker2008,
title={{DECOMP}—from interpreting mass spectrometry peaks to solving the Money Changing Problem},
author={B{\"o}cker, Sebastian and Lipt{\'a}k, Zsuzsanna and Martin, Marcel and Pervukhin, Anton and Sudek, Henner},
journal={Bioinformatics},
volume={24},
number={4},
pages={591-593},
year={2008},
publisher={Oxford Univ Press}}
@article{Zhang2016,
title={Parallel formula generator based on branch-and-bound algorithm for elucidating high resolution mass spectra},
author={Zhang, Mingjing and Zhang, Zhimin and Chen, Chen and Lu, Hongmei and Liang, Yizeng},