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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. Research article

    Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library

    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...

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

    Journal of Cheminformatics 2017 9:19

    Published on: 15 March 2017

  8. Database

    ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics

    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...

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

    Journal of Cheminformatics 2017 9:17

    Published on: 7 March 2017

  9. Research article

    Predicting drug–drug interactions through drug structural similarities and interaction networks incorporating pharmacokinetics and pharmacodynamics knowledge

    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...

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

    Journal of Cheminformatics 2017 9:16

    Published on: 7 March 2017

  10. Methodology

    Large-scale virtual screening on public cloud resources with Apache Spark

    Structure-based virtual screening is an in-silico method to screen a target receptor against a virtual molecular library. Applying docking-based screening to large molecular libraries can be computationally e...

    Marco Capuccini, Laeeq Ahmed, Wesley Schaal, Erwin Laure and Ola Spjuth

    Journal of Cheminformatics 2017 9:15

    Published on: 6 March 2017

  11. Research article

    Modeling framework for isotopic labeling of heteronuclear moieties

    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...

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

    Journal of Cheminformatics 2017 9:14

    Published on: 4 March 2017

  12. Commentary

    Technical implications of new IUPAC elements in cheminformatics

    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...

    John W. Mayfield and Roger A. Sayle

    Journal of Cheminformatics 2017 9:10

    Published on: 13 February 2017

  13. Preliminary communication

    Database fingerprint (DFP): an approach to represent molecular databases

    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...

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

    Journal of Cheminformatics 2017 9:9

    Published on: 6 February 2017

  14. Research article

    Mapping and classifying molecules from a high-throughput structural database

    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...

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

    Journal of Cheminformatics 2017 9:6

    Published on: 2 February 2017

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