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  1. Research article

    Deep-learning: investigating deep neural networks hyper-parameters and comparison of performance to shallow methods for modeling bioactivity data

    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...

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

    Journal of Cheminformatics 2017 9:42

    Published on: 28 June 2017

  2. Research article

    Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D

    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 ...

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

    Journal of Cheminformatics 2017 9:39

    Published on: 14 June 2017

  3. Software

    chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery

    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...

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

    Journal of Cheminformatics 2017 9:38

    Published on: 12 June 2017

  4. Software

    QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations

    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...

    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

    Journal of Cheminformatics 2017 9:35

    Published on: 7 June 2017

  5. Methodology

    An algorithm to identify functional groups in organic molecules

    The concept of functional groups forms a basis of organic chemistry, medicinal chemistry, toxicity assessment, spectroscopy and also chemical nomenclature. All current software systems to identify functional g...

    Peter Ertl

    Journal of Cheminformatics 2017 9:36

    Published on: 7 June 2017

  6. Software

    The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

    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 ...

    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

    Journal of Cheminformatics 2017 9:33

    Published on: 6 June 2017

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

  7. Research article

    Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy

    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 ...

    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

    Journal of Cheminformatics 2017 9:32

    Published on: 25 May 2017

  8. Research article

    Electronic lab notebooks: can they replace paper?

    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...

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

    Journal of Cheminformatics 2017 9:31

    Published on: 24 May 2017

  9. Software

    Scaffold Hunter: a comprehensive visual analytics framework for drug discovery

    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...

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

    Journal of Cheminformatics 2017 9:28

    Published on: 11 May 2017

  10. Software

    ChemSAR: an online pipelining platform for molecular SAR modeling

    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...

    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

    Journal of Cheminformatics 2017 9:27

    Published on: 4 May 2017

  11. Research article

    Comparative analyses of structural features and scaffold diversity for purchasable compound libraries

    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...

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

    Journal of Cheminformatics 2017 9:25

    Published on: 21 April 2017

  12. Research article

    Critical Assessment of Small Molecule Identification 2016: automated methods

    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...

    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…

    Journal of Cheminformatics 2017 9:22

    Published on: 27 March 2017

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