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  1. Content type: Review

    Recent developments in metabolic engineering have led to the successful biosynthesis of valuable products, such as the precursor of the antimalarial compound, artemisinin, and opioid precursor, thebaine. Synth...

    Authors: Sarah M. Kim, Matthew I. Peña, Mark Moll, George N. Bennett and Lydia E. Kavraki

    Citation: Journal of Cheminformatics 2017 9:51

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  2. Content type: Research Article

    GPU acceleration is useful in solving complex chemical information problems. Identifying unknown structures from the mass spectra of natural product mixtures has been a desirable yet unresolved issue in metabo...

    Authors: Alioune Schurz, Bo-Han Su, Yi-Shu Tu, Tony Tsung-Yu Lu, Olivia A. Lin and Yufeng J. Tseng

    Citation: Journal of Cheminformatics 2017 9:50

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  3. Content type: Preliminary communication

    On the one hand, ligand efficiency (LE) and the binding efficiency index (BEI), which are binding properties (B) averaged versus the heavy atom count (HAC: LE) or molecular weight (MW: BEI), have recently been...

    Authors: Jaroslaw Polanski, Aleksandra Tkocz and Urszula Kucia

    Citation: Journal of Cheminformatics 2017 9:49

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  4. Content type: Research article

    This work introduces a method to tune a sequence-based generative model for molecular de novo design that through augmented episodic likelihood can learn to generate structures with certain specified desirable...

    Authors: Marcus Olivecrona, Thomas Blaschke, Ola Engkvist and Hongming Chen

    Citation: Journal of Cheminformatics 2017 9:48

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  5. Content type: Research article

    Self-interactions Proteins (SIPs) is important for their biological activity owing to the inherent interaction amongst their secondary structures or domains. However, due to the limitations of experimental Sel...

    Authors: Ji-Yong An, Lei Zhang, Yong Zhou, Yu-Jun Zhao and Da-Fu Wang

    Citation: Journal of Cheminformatics 2017 9:47

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  6. Content type: Research article

    Natural products represent a prominent source of pharmaceutically and industrially important agents. Calculating the chemical similarity of two molecules is a central task in cheminformatics, with applications...

    Authors: Michael A. Skinnider, Chris A. Dejong, Brian C. Franczak, Paul D. McNicholas and Nathan A. Magarvey

    Citation: Journal of Cheminformatics 2017 9:46

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  7. Content type: Research article

    The increase of publicly available bioactivity data in recent years has fueled and catalyzed research in chemogenomics, data mining, and modeling approaches. As a direct result, over the past few years a multi...

    Authors: Eelke B. Lenselink, Niels ten Dijke, Brandon Bongers, George Papadatos, Herman W. T. van Vlijmen, Wojtek Kowalczyk, Adriaan P. IJzerman and Gerard J. P. van Westen

    Citation: Journal of Cheminformatics 2017 9:45

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  8. Content type: Research article

    The goal of defining an applicability domain for a predictive classification model is to identify the region in chemical space where the model’s predictions are reliable. The boundary of the applicability doma...

    Authors: Waldemar Klingspohn, Miriam Mathea, Antonius ter Laak, Nikolaus Heinrich and Knut Baumann

    Citation: Journal of Cheminformatics 2017 9:44

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  9. Content type: Research article

    Drug design of protein kinase inhibitors is now greatly enabled by thousands of publicly available X-ray structures, extensive ligand binding data, and optimized scaffolds coming off patent. The extensive dat...

    Authors: Dilip Narayanan, Osman A. B. S. M. Gani, Franz X. E. Gruber and Richard A. Engh

    Citation: Journal of Cheminformatics 2017 9:43

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  10. Content type: Research article

    In recent years, research in artificial neural networks has resurged, now under the deep-learning umbrella, and grown extremely popular. Recently reported success of DL techniques in crowd-sourced QSAR and pre...

    Authors: Alexios Koutsoukas, Keith J. Monaghan, Xiaoli Li and Jun Huan

    Citation: Journal of Cheminformatics 2017 9:42

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  11. Content type: Erratum

    Authors: Jiangming Sun, Nina Jeliazkova, Vladimir Chupakhin, Jose-Felipe Golib-Dzib, Ola Engkvist, Lars Carlsson, Jörg Wegner, Hugo Ceulemans, Ivan Georgiev, Vedrin Jeliazkov, Nikolay Kochev, Thomas J. Ashby and Hongming Chen

    Citation: Journal of Cheminformatics 2017 9:41

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    The original article was published in Journal of Cheminformatics 2017 9:17

  12. Content type: Research article

    The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same element in a product ...

    Authors: German A. Preciat Gonzalez, Lemmer R. P. El Assal, Alberto Noronha, Ines Thiele, Hulda S. Haraldsdóttir and Ronan M. T. Fleming

    Citation: Journal of Cheminformatics 2017 9:39

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  13. Content type: Software

    Analyzing files containing chemical information is at the core of cheminformatics. Each analysis may require a unique workflow. This paper describes the chemalot and chemalot_knime open source packages. Chemal...

    Authors: Man-Ling Lee, Ignacio Aliagas, Jianwen A. Feng, Thomas Gabriel, T. J. O’Donnell, Benjamin D. Sellers, Bernd Wiswedel and Alberto Gobbi

    Citation: Journal of Cheminformatics 2017 9:38

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  14. Content type: Software

    In previous reports, Marrero-Ponce et al. proposed algebraic formalisms for characterizing topological (2D) and chiral (2.5D) molecular features through atom- and bond-based ToMoCoMD-CARDD (acronym for Topolo...

    Authors: José R. Valdés-Martiní, Yovani Marrero-Ponce, César R. García-Jacas, Karina Martinez-Mayorga, Stephen J. Barigye, Yasser Silveira Vaz d‘Almeida, Hai Pham-The, Facundo Pérez-Giménez and Carlos A. Morell

    Citation: Journal of Cheminformatics 2017 9:35

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  15. Content type: Research article

    An important aspect of chemoinformatics and material-informatics is the usage of machine learning algorithms to build Quantitative Structure Activity Relationship (QSAR) models. The RANdom SAmple Consensus (RA...

    Authors: Omer Kaspi, Abraham Yosipof and Hanoch Senderowitz

    Citation: Journal of Cheminformatics 2017 9:34

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  16. Content type: Software

    The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform ...

    Authors: Egon L. Willighagen, John W. Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomáš Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain Torrance, Chris T. Evelo, Rajarshi Guha and Christoph Steinbeck

    Citation: Journal of Cheminformatics 2017 9:33

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    The Erratum to this article has been published in Journal of Cheminformatics 2017 9:53

  17. Content type: Research article

    In mass spectrometry-based untargeted metabolomics, rarely more than 30% of the compounds are identified. Without the true identity of these molecules it is impossible to draw conclusions about the biological ...

    Authors: Ivana Blaženović, Tobias Kind, Hrvoje Torbašinović, Slobodan Obrenović, Sajjan S. Mehta, Hiroshi Tsugawa, Tobias Wermuth, Nicolas Schauer, Martina Jahn, Rebekka Biedendieck, Dieter Jahn and Oliver Fiehn

    Citation: Journal of Cheminformatics 2017 9:32

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  18. Content type: Research article

    Despite the increasingly digital nature of society there are some areas of research that remain firmly rooted in the past; in this case the laboratory notebook, the last remaining paper component of an experim...

    Authors: Samantha Kanza, Cerys Willoughby, Nicholas Gibbins, Richard Whitby, Jeremy Graham Frey, Jana Erjavec, Klemen Zupančič, Matjaž Hren and Katarina Kovač

    Citation: Journal of Cheminformatics 2017 9:31

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  19. Content type: Software

    CPANNatNIC is software for development of counter-propagation artificial neural network models. Besides the interface for training of a new neural network it also provides an interface for visualisation of the...

    Authors: Viktor Drgan, Špela Župerl, Marjan Vračko, Claudia Ileana Cappelli and Marjana Novič

    Citation: Journal of Cheminformatics 2017 9:30

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  20. Content type: Software

    The era of big data is influencing the way how rational drug discovery and the development of bioactive molecules is performed and versatile tools are needed to assist in molecular design workflows. Scaffold H...

    Authors: Till Schäfer, Nils Kriege, Lina Humbeck, Karsten Klein, Oliver Koch and Petra Mutzel

    Citation: Journal of Cheminformatics 2017 9:28

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  21. Content type: Software

    In recent years, predictive models based on machine learning techniques have proven to be feasible and effective in drug discovery. However, to develop such a model, researchers usually have to combine multipl...

    Authors: Jie Dong, Zhi-Jiang Yao, Min-Feng Zhu, Ning-Ning Wang, Ben Lu, Alex F. Chen, Ai-Ping Lu, Hongyu Miao, Wen-Bin Zeng and Dong-Sheng Cao

    Citation: Journal of Cheminformatics 2017 9:27

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  22. Content type: Research article

    Patents are an important source of information for effective decision making in drug discovery. Encouragingly, freely accessible patent-chemistry databases are now in the public domain. However, at present the...

    Authors: Stefan Senger

    Citation: Journal of Cheminformatics 2017 9:26

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  23. Content type: Research article

    Large purchasable screening libraries of small molecules afforded by commercial vendors are indispensable sources for virtual screening (VS). Selecting an optimal screening library for a specific VS campaign i...

    Authors: Jun Shang, Huiyong Sun, Hui Liu, Fu Chen, Sheng Tian, Peichen Pan, Dan Li, Dexin Kong and Tingjun Hou

    Citation: Journal of Cheminformatics 2017 9:25

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  24. Content type: Research article

    Computational prediction of the interaction between drugs and targets is a standing challenge in the field of drug discovery. A number of rather accurate predictions were reported for various binary drug–targe...

    Authors: Tong He, Marten Heidemeyer, Fuqiang Ban, Artem Cherkasov and Martin Ester

    Citation: Journal of Cheminformatics 2017 9:24

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  25. Content type: Research article

    The algorithmic, large-scale use and analysis of reaction databases such as Reaxys is currently hindered by the absence of widely adopted standards for publishing reaction data in machine readable formats. Cru...

    Authors: Philipp-Maximilian Jacob, Tian Lan, Jonathan M. Goodman and Alexei A. Lapkin

    Citation: Journal of Cheminformatics 2017 9:23

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  26. Content type: Research article

    The fourth round of the Critical Assessment of Small Molecule Identification (CASMI) Contest (www.​casmi-contest.​org) was held in 2016, with two new cat...

    Authors: Emma L. Schymanski, Christoph Ruttkies, Martin Krauss, Céline Brouard, Tobias Kind, Kai Dührkop, Felicity Allen, Arpana Vaniya, Dries Verdegem, Sebastian Böcker, Juho Rousu, Huibin Shen, Hiroshi Tsugawa, Tanvir Sajed, Oliver Fiehn, Bart Ghesquière…

    Citation: Journal of Cheminformatics 2017 9:22

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  27. Content type: Methodology

    The accuracy of any 3D-QSAR, Pharmacophore and 3D-similarity based chemometric target fishing models are highly dependent on a reasonable sample of active conformations. Since a number of diverse conformationa...

    Authors: Hyoungrae Kim, Cheongyun Jang, Dharmendra K. Yadav and Mi-hyun Kim

    Citation: Journal of Cheminformatics 2017 9:21

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  28. Content type: Research article

    Liquid chromatography coupled with electrospray ionization tandem mass spectrometry (LC–ESI–MS/MS) is used for comprehensive metabolome and lipidome analyses. Compound identification relies on similarity match...

    Authors: Hiroshi Tsugawa, Kazutaka Ikeda, Wataru Tanaka, Yuya Senoo, Makoto Arita and Masanori Arita

    Citation: Journal of Cheminformatics 2017 9:19

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  29. Content type: Research article

    In previous work, we have assessed the structural similarities between marketed drugs (‘drugs’) and endogenous natural human metabolites (‘metabolites’ or ‘endogenites’), using ‘fingerprint’ methods in common...

    Authors: Steve O’Hagan and Douglas B. Kell

    Citation: Journal of Cheminformatics 2017 9:18

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  30. Content type: Database

    Chemogenomics data generally refers to the activity data of chemical compounds on an array of protein targets and represents an important source of information for building in silico target prediction models. The...

    Authors: Jiangming Sun, Nina Jeliazkova, Vladimir Chupakhin, Jose-Felipe Golib-Dzib, Ola Engkvist, Lars Carlsson, Jörg Wegner, Hugo Ceulemans, Ivan Georgiev, Vedrin Jeliazkov, Nikolay Kochev, Thomas J. Ashby and Hongming Chen

    Citation: Journal of Cheminformatics 2017 9:17

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    The Erratum to this article has been published in Journal of Cheminformatics 2017 9:41

  31. Content type: Research article

    Drug–drug interactions (DDIs) may lead to adverse effects and potentially result in drug withdrawal from the market. Predicting DDIs during drug development would help reduce development costs and time by rigo...

    Authors: Takako Takeda, Ming Hao, Tiejun Cheng, Stephen H. Bryant and Yanli Wang

    Citation: Journal of Cheminformatics 2017 9:16

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  32. Content type: Research article

    Isotopic labeling is an analytic technique that is used to track the movement of isotopes through reaction networks. In general, the applicability of isotopic labeling techniques is limited to the investigatio...

    Authors: Mark I. Borkum, Patrick N. Reardon, Ronald C. Taylor and Nancy G. Isern

    Citation: Journal of Cheminformatics 2017 9:14

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  33. Content type: Methodology

    Several web-based tools have been reported recently which predict the possible targets of a small molecule by similarity to compounds of known bioactivity using molecular fingerprints (fps), however predictio...

    Authors: Mahendra Awale and Jean-Louis Reymond

    Citation: Journal of Cheminformatics 2017 9:11

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  34. Content type: Commentary

    The symbols for the new IUPAC elements named in November 2016 can introduce subtle ambiguities within cheminformatics software. The ambiguities are described and demonstrated by highlighting inconsistencies be...

    Authors: John W. Mayfield and Roger A. Sayle

    Citation: Journal of Cheminformatics 2017 9:10

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  35. Content type: Preliminary communication

    Molecular fingerprints are widely used in several areas of chemoinformatics including diversity analysis and similarity searching. The fingerprint-based analysis of chemical libraries, in particular of large c...

    Authors: Eli Fernández-de Gortari, César R. García-Jacas, Karina Martinez-Mayorga and José L. Medina-Franco

    Citation: Journal of Cheminformatics 2017 9:9

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  36. Content type: Research article

    A new metric for the evaluation of model performance in the field of virtual screening and quantitative structure–activity relationship applications is described. This metric has been termed the power metric a...

    Authors: Julio Cesar Dias Lopes, Fábio Mendes dos Santos, Andrelly Martins-José, Koen Augustyns and Hans De Winter

    Citation: Journal of Cheminformatics 2017 9:7

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    The Commentary to this article has been published in Journal of Cheminformatics 2018 10:13

  37. Content type: Research article

    High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and p...

    Authors: Sandip De, Felix Musil, Teresa Ingram, Carsten Baldauf and Michele Ceriotti

    Citation: Journal of Cheminformatics 2017 9:6

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  38. Content type: Database

    Skin sensitization is an important toxicological endpoint for chemical hazard determination and safety assessment. Prediction of chemical skin sensitizer had traditionally relied on data from rodent models. Th...

    Authors: Chia-Chi Wang, Ying-Chi Lin, Shan-Shan Wang, Chieh Shih, Yi-Hui Lin and Chun-Wei Tung

    Citation: Journal of Cheminformatics 2017 9:5

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  39. Content type: Research article

    The design and use of a metadata-driven data repository for research data management is described. Metadata is collected automatically during the submission process whenever possible and is registered with Dat...

    Authors: Matthew J. Harvey, Andrew McLean and Henry S. Rzepa

    Citation: Journal of Cheminformatics 2017 9:4

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  40. Content type: Database

    Sigma (σ) receptors are accepted as a particular receptor class consisting of two subtypes: sigma-1 (σ1) and sigma-2 (σ2). The two receptor subtypes have specific drug actions, pharmacological profiles and molec...

    Authors: Giovanni Nastasi, Carla Miceli, Valeria Pittalà, Maria N. Modica, Orazio Prezzavento, Giuseppe Romeo, Antonio Rescifina, Agostino Marrazzo and Emanuele Amata

    Citation: Journal of Cheminformatics 2017 9:3

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  41. Content type: Database

    Natural products have increasingly attracted much attention as a valuable resource for the development of anticancer medicines due to the structural novelty and good bioavailability. This necessitates a compr...

    Authors: Hwanho Choi, Sun Young Cho, Ho Jeong Pak, Youngsoo Kim, Jung-yun Choi, Yoon Jae Lee, Byung Hee Gong, Yeon Seok Kang, Taehoon Han, Geunbae Choi, Yeeun Cho, Soomin Lee, Dekwoo Ryoo and Hwangseo Park

    Citation: Journal of Cheminformatics 2017 9:2

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