TY - STD TI - Engel T, Gasteiger J (2018) Chemoinformatics: basic concepts and methods, chap 4. Wiley-VCH Verlag GmbH ID - ref1 ER - TY - BOOK AU - Karthikeyan, M. AU - Vyas, R. PY - 2014 DA - 2014// TI - Practical chemoinformatics, chap 6 PB - Springer CY - New Delhi UR - https://doi.org/10.1007/978-81-322-1780-0 DO - 10.1007/978-81-322-1780-0 ID - Karthikeyan2014 ER - TY - STD TI - Faulon J-L, Bender A (2010) Handbook of chemoinformatics algorithms, chap 11. CRC Press ID - ref3 ER - TY - STD TI - Daylight. SMIRKS: A Reaction Transform Language [Internet] [cited 2017 Dec 20]. http://www.daylight.com/dayhtml/doc/theory/theory.smirks.html UR - http://www.daylight.com/dayhtml/doc/theory/theory.smirks.html ID - ref4 ER - TY - STD TI - Daylight. SMARTS: a language for describing molecular patterns [Internet] [cited 2017 Sep 19]. http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html UR - http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html ID - ref5 ER - TY - JOUR AU - Homer, R. W. AU - Swanson, J. AU - Jilek, R. J. AU - Hurst, T. AU - Clark, R. D. PY - 2008 DA - 2008// TI - SYBYL line notation (SLN): a single notation to represent chemical structures, queries, reactions, and virtual libraries JO - J Chem Inf Model VL - 48 UR - https://doi.org/10.1021/ci7004687 DO - 10.1021/ci7004687 ID - Homer2008 ER - TY - JOUR AU - Grethe, G. AU - Goodman, J. AU - Allen, C. PY - 2013 DA - 2013// TI - International chemical identifier for chemical reactions JO - J Cheminform VL - O5 ID - Grethe2013 ER - TY - STD TI - Elsevier MDL. CTFile formats. Mdl. 2005 (June) ID - ref8 ER - TY - JOUR AU - Yang, C. AU - Tarkhov, A. AU - Marusczyk, J. AU - Bienfait, B. AU - Gasteiger, J. AU - Kleinoeder, T. PY - 2015 DA - 2015// TI - New publicly available chemical query language, CSRML, to support chemotype representations for application to data mining and modeling JO - J Chem Inf Model VL - 55 UR - https://doi.org/10.1021/ci500667v DO - 10.1021/ci500667v ID - Yang2015 ER - TY - JOUR AU - Holliday, G. L. AU - Murray-Rust, P. AU - Rzepa, H. S. PY - 2006 DA - 2006// TI - Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions JO - J Chem Inf Model VL - 46 UR - https://doi.org/10.1021/ci0502698 DO - 10.1021/ci0502698 ID - Holliday2006 ER - TY - STD TI - Chemical Markup Language|CML [Internet] [cited 2017 Dec 18]. http://www.xml-cml.org/ UR - http://www.xml-cml.org/ ID - ref11 ER - TY - JOUR AU - Reisen, F. H. AU - Schneider, G. AU - Proschak, E. PY - 2009 DA - 2009// TI - Reaction-MQL: line notation for functional transformation JO - J Chem Inf Model VL - 49 UR - https://doi.org/10.1021/ci800215t DO - 10.1021/ci800215t ID - Reisen2009 ER - TY - JOUR AU - Proschak, E. AU - Wegner, J. K. AU - Schüller, A. AU - Schneider, G. AU - Fechner, U. PY - 2007 DA - 2007// TI - Molecular Query Language (MQL)—a context-free grammar for substructure matching JO - J Chem Inf Model VL - 47 UR - https://doi.org/10.1021/ci600305h DO - 10.1021/ci600305h ID - Proschak2007 ER - TY - STD TI - Pirok G, Máté N, Dóránt S, Vargyas M, Csizmadia F (2004) How can generic reactions be specific? Virtual synthesis with “smart” reactions ChemAxon [Internet]. https://chemaxon.com/poster UR - https://chemaxon.com/poster ID - ref14 ER - TY - JOUR AU - Steinbeck, C. AU - Han, Y. AU - Kuhn, S. AU - Horlacher, O. AU - Luttmann, E. AU - Willighagen, E. PY - 2003 DA - 2003// TI - The Chemistry Development Kit (CDK): an open-source Java library for chemo- and bioinformatics JO - J Chem Inf Comput Sci VL - 43 UR - https://doi.org/10.1021/ci025584y DO - 10.1021/ci025584y ID - Steinbeck2003 ER - TY - JOUR AU - Steinbeck, C. AU - Hoppe, C. AU - Kuhn, S. AU - Floris, M. AU - Guha, R. AU - Willighagen, E. L. PY - 2006 DA - 2006// TI - Recent developments of the chemistry development kit (CDK)—an open-source java library for chemo- and bioinformatics JO - Curr Pharm Des VL - 12 UR - https://doi.org/10.2174/138161206777585274 DO - 10.2174/138161206777585274 ID - Steinbeck2006 ER - TY - JOUR AU - Willighagen, E. L. AU - Mayfield, J. W. AU - Alvarsson, J. AU - Berg, A. AU - Carlsson, L. AU - Jeliazkova, N. PY - 2017 DA - 2017// TI - The chemistry development kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching JO - J Cheminform VL - 9 UR - https://doi.org/10.1186/s13321-016-0187-6 DO - 10.1186/s13321-016-0187-6 ID - Willighagen2017 ER - TY - JOUR AU - O’Boyle, N. M. AU - Banck, M. AU - James, C. A. AU - Morley, C. AU - Vandermeersch, T. AU - Hutchison, G. R. PY - 2011 DA - 2011// TI - Open babel: an open chemical toolbox JO - J Cheminform VL - 3 ID - O’Boyle2011 ER - TY - STD TI - Landrum G (2017) RDKit documentation [Internet]. http://www.rdkit.org/RDKit_Docs.current.pdf UR - http://www.rdkit.org/RDKit_Docs.current.pdf ID - ref19 ER - TY - STD TI - OEChem Toolkit: Reactions [Internet]. OpenEye Scientific. [cited 2017 Sep 12]. https://docs.eyesopen.com/toolkits/python/oechemtk/reactions.html UR - https://docs.eyesopen.com/toolkits/python/oechemtk/reactions.html ID - ref20 ER - TY - STD TI - Daylight. Reaction toolkit [Internet] [cited 2017 Sep 12]. http://www.daylight.com/products/reaction_kit.html UR - http://www.daylight.com/products/reaction_kit.html ID - ref21 ER - TY - JOUR AU - Ihlenfeldt, W. D. AU - Takahashi, Y. AU - Abe, H. AU - Sasaki, S. PY - 1994 DA - 1994// TI - Computation and management of chemical properties in CACTVS: an extensible networked approach toward modularity and compatibility JO - J Chem Inf Comput Sci VL - 34 UR - https://doi.org/10.1021/ci00017a013 DO - 10.1021/ci00017a013 ID - Ihlenfeldt1994 ER - TY - STD TI - Reactor: a high performance virtual synthesis engine [Internet]. ChemAxon. [cited 2017 Sep 12]. https://www.chemaxon.com/products/reactor/ UR - https://www.chemaxon.com/products/reactor/ ID - ref23 ER - TY - STD TI - JChem for Office [Internet]. ChemAxon. [cited 2017 Sep 19]. https://www.chemaxon.com/products/jchem-for-office/ UR - https://www.chemaxon.com/products/jchem-for-office/ ID - ref24 ER - TY - STD TI - MolEngine: .NET Cheminformatics toolkit [Internet] [cited 2017 Sep 19]. http://www2.scilligence.com/web/molengine.aspx UR - http://www2.scilligence.com/web/molengine.aspx ID - ref25 ER - TY - STD TI - MOE: Molecular Operating Environment [Internet]. Chemical Computing Group. [cited 2017 Sep 19]. https://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm UR - https://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm ID - ref26 ER - TY - STD TI - Accord Software Development Kit [Internet]. Accelrys. [cited 2017 Dec 20]. http://accelrys.com/resource-center/downloads/updates/accord/sdk/sdk615/sdk615.html UR - http://accelrys.com/resource-center/downloads/updates/accord/sdk/sdk615/sdk615.html ID - ref27 ER - TY - JOUR AU - Patlewicz, G. AU - Jeliazkova, N. AU - Safford, R. J. AU - Worth, A. P. AU - Aleksiev, B. PY - 2008 DA - 2008// TI - An evaluation of the implementation of the Cramer classification scheme in the Toxtree software JO - SAR QSAR Environ Res VL - 19 UR - https://doi.org/10.1080/10629360802083871 DO - 10.1080/10629360802083871 ID - Patlewicz2008 ER - TY - JOUR AU - Rydberg, P. AU - Gloriam, D. E. AU - Zaretzki, J. AU - Breneman, C. AU - Olsen, L. PY - 2010 DA - 2010// TI - SMARTCyp: a 2D method for prediction of cytochrome P450-mediated drug metabolism JO - ACS Med Chem Lett VL - 1 UR - https://doi.org/10.1021/ml100016x DO - 10.1021/ml100016x ID - Rydberg2010 ER - TY - JOUR AU - Jeliazkova, N. AU - Kochev, N. PY - 2011 DA - 2011// TI - AMBIT-SMARTS: efficient searching of chemical structures and fragments JO - Mol Inform VL - 30 ID - Jeliazkova2011 ER - TY - JOUR AU - Jeliazkova, N. AU - Jeliazkov, V. PY - 2011 DA - 2011// TI - AMBIT RESTful web services: an implementation of the OpenTox Application Programming Interface JO - J Cheminform VL - 3 UR - https://doi.org/10.1186/1758-2946-3-18 DO - 10.1186/1758-2946-3-18 ID - Jeliazkova2011 ER - TY - STD TI - Ideaconsult Ltd. AMBIT [Internet]. http://ambit.sourceforge.net/ UR - http://ambit.sourceforge.net/ ID - ref32 ER - TY - JOUR AU - Jeliazkova, N. AU - Koch, V. AU - Li, Q. AU - Jensch, U. AU - Reigl, J. S. AU - Kreiling, R. PY - 2016 DA - 2016// TI - Linking LRI AMBIT chemoinformatic system with the IUCLID substance database to support read-across of substance endpoint data and category formation JO - Toxicol Lett VL - 258 UR - https://doi.org/10.1016/j.toxlet.2016.06.1469 DO - 10.1016/j.toxlet.2016.06.1469 ID - Jeliazkova2016 ER - TY - STD TI - Ideaconsult Ltd. LRI AMBIT tool for read across [Internet]. https://ambitlri.ideaconsult.net/ UR - https://ambitlri.ideaconsult.net/ ID - ref34 ER - TY - STD TI - Smith M, March J (2007) March’s advanced organic chemistry: reactions, mechanisms and structure, chap 4, 6th edn. Wiley ID - ref35 ER - TY - STD TI - SMILES—a simplified chemical language [Internet]. Daylight theory. 2008 [cited 2017 Sep 19]. http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html UR - http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html ID - ref36 ER - TY - JOUR AU - Munro, I. AU - Ford, R. A. AU - Kennepohl, E. AU - Sprenger, J. PY - 1996 DA - 1996// TI - Correlation of structural class with no-observed-effect-levels: a proposal for establishing a threshold of concern JO - Food Chem Toxicol VL - 34 UR - https://doi.org/10.1016/S0278-6915(96)00049-X DO - 10.1016/S0278-6915(96)00049-X ID - Munro1996 ER - TY - STD TI - Avramova S, Kochev N, Angelov P. RetroTransformDB: a dataset of generic transforms for retrosynthetic analysis. Data [Internet]. 2018 Apr 21 [cited 2018 Jul 28]; 3(2):14. http://www.mdpi.com/2306-5729/3/2/14 UR - http://www.mdpi.com/2306-5729/3/2/14 ID - ref38 ER - TY - STD TI - Avramova S, Kochev N, Angelov P. RetroTransformDB—a dataset of transforms (retrosynthetic reactions). 2018 Mar 28 [cited 2018 Jul 28]. https://zenodo.org/record/1209313#.W1xo4MJdLIU UR - https://zenodo.org/record/1209313#.W1xo4MJdLIU ID - ref39 ER - TY - STD TI - Toxtree—Toxic hazard estimation by decision tree approach [Internet]. http://toxtree.sourceforge.net/ UR - http://toxtree.sourceforge.net/ ID - ref40 ER - TY - JOUR AU - Wicker, J. AU - Lorsbach, T. AU - Gütlein, M. AU - Schmid, E. AU - Latino, D. AU - Kramer, S. PY - 2016 DA - 2016// TI - enviPath—the environmental contaminant biotransformation pathway resource JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1229 DO - 10.1093/nar/gkv1229 ID - Wicker2016 ER - TY - STD TI - Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, Vázquez-Fresno R et al. HMDB 4.0: the human metabolome database for 2018. Nucleic Acids Res [Internet]. 2017 Nov 11. http://academic.oup.com/nar/article/doi/10.1093/nar/gkx1089/4616873 UR - http://academic.oup.com/nar/article/doi/10.1093/nar/gkx1089/4616873 ID - ref42 ER - TY - STD TI - Feunang YD. Cheminformatics tools for enabling metabolomics [Internet]. https://era.library.ualberta.ca/files/crf55z804r/DjoumbouFeunang_Yannick_201709_PhD.pdf UR - https://era.library.ualberta.ca/files/crf55z804r/DjoumbouFeunang_Yannick_201709_PhD.pdf ID - ref43 ER - TY - STD TI - Jeliazkova N, Kochev N, Jeliazkov V. ambitcli-3.0.2 [Internet]. 2016 [cited 2017 Dec 19]. https://zenodo.org/record/173560#.WjlcRyvfHVq UR - https://zenodo.org/record/173560#.WjlcRyvfHVq ID - ref44 ER - TY - JOUR AU - Sun, J. AU - Jeliazkova, N. AU - Chupakhin, V. AU - Golib-Dzib, J. -. F. AU - Engkvist, O. AU - Carlsson, L. PY - 2017 DA - 2017// TI - ExCAPE-DB: an integrated large scale dataset facilitating big data analysis in chemogenomics JO - J Cheminform VL - 9 UR - https://doi.org/10.1186/s13321-017-0203-5 DO - 10.1186/s13321-017-0203-5 ID - Sun2017 ER - TY - JOUR AU - Kochev, N. AU - Avramova, S. AU - Jeliazkova, N. PY - 2017 DA - 2017// TI - Combinatorial generation of molecules by virtual software reactor JO - Sci Work Union Sci Bulg Plovdiv VL - 11 ID - Kochev2017 ER -