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  1. Software

    Chemotion ELN: an Open Source electronic lab notebook for chemists in academia

    The development of an electronic lab notebook (ELN) for researchers working in the field of chemical sciences is presented. The web based application is available as an Open Source software that offers modern ...

    Pierre Tremouilhac, An Nguyen, Yu-Chieh Huang, Serhii Kotov, Dominic Sebastian Lütjohann, Florian Hübsch, Nicole Jung and Stefan Bräse

    Journal of Cheminformatics 2017 9:54

    Published on: 25 September 2017

  2. Erratum

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

    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 9:53

    Published on: 20 September 2017

    The original article was published in Journal of Cheminformatics 2017 9:33

  3. Software

    Scoria: a Python module for manipulating 3D molecular data

    Third-party packages have transformed the Python programming language into a powerful computational-biology tool. Package installation is easy for experienced users, but novices sometimes struggle with depende...

    Patrick Ropp, Aaron Friedman and Jacob D. Durrant

    Journal of Cheminformatics 2017 9:52

    Published on: 18 September 2017

  4. Review

    A review of parameters and heuristics for guiding metabolic pathfinding

    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...

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

    Journal of Cheminformatics 2017 9:51

    Published on: 15 September 2017

  5. Research Article

    G.A.M.E.: GPU-accelerated mixture elucidator

    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...

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

    Journal of Cheminformatics 2017 9:50

    Published on: 15 September 2017

  6. Research article

    Molecular de-novo design through deep reinforcement learning

    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...

    Marcus Olivecrona, Thomas Blaschke, Ola Engkvist and Hongming Chen

    Journal of Cheminformatics 2017 9:48

    Published on: 4 September 2017

  7. Research article

    Computational methods using weighed-extreme learning machine to predict protein self-interactions with protein evolutionary information

    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...

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

    Journal of Cheminformatics 2017 9:47

    Published on: 18 August 2017

  8. Research article

    Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm

    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...

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

    Journal of Cheminformatics 2017 9:46

    Published on: 16 August 2017

  9. Research article

    Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set

    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...

    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

    Journal of Cheminformatics 2017 9:45

    Published on: 14 August 2017

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

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