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  1. Research article

    An automated framework for QSAR model building

    In-silico quantitative structure–activity relationship (QSAR) models based tools are widely used to screen huge databases of compounds in order to determine the biological properties of chemical molecules base...

    Samina Kausar and Andre O. Falcao

    Journal of Cheminformatics 2018 10:1

    Published on: 16 January 2018

  2. Research article

    Computer-aided design of multi-target ligands at A1R, A2AR and PDE10A, key proteins in neurodegenerative diseases

    Compounds designed to display polypharmacology may have utility in treating complex diseases, where activity at multiple targets is required to produce a clinical effect. In particular, suitable compounds may ...

    Leen Kalash, Cristina Val, Jhonny Azuaje, María I. Loza, Fredrik Svensson, Azedine Zoufir, Lewis Mervin, Graham Ladds, José Brea, Robert Glen, Eddy Sotelo and Andreas Bender

    Journal of Cheminformatics 2017 9:67

    Published on: 30 December 2017

  3. Methodology

    Systematic exploration of multiple drug binding sites

    Targets with multiple (prerequisite or allosteric) binding sites have an increasing importance in drug design. Experimental determination of atomic resolution structures of ligands weakly bound to multiple bin...

    Mónika Bálint, Norbert Jeszenői, István Horváth, David van der Spoel and Csaba Hetényi

    Journal of Cheminformatics 2017 9:65

    Published on: 28 December 2017

  4. Research article

    Can human experts predict solubility better than computers?

    In this study, we design and carry out a survey, asking human experts to predict the aqueous solubility of druglike organic compounds. We investigate whether these experts, drawn largely from the pharmaceutica...

    Samuel Boobier, Anne Osbourn and John B. O. Mitchell

    Journal of Cheminformatics 2017 9:63

    Published on: 13 December 2017

  5. Software

    BoBER: web interface to the base of bioisosterically exchangeable replacements

    We describe a novel freely available web server Base of Bioisosterically Exchangeable Replacements (BoBER), which implements an interface to a database of bioisosteric and scaffold hopping replacements. Bioiso...

    Samo Lešnik, Blaž Škrlj, Nika Eržen, Urban Bren, Stanislav Gobec, Janez Konc and Dušanka Janežič

    Journal of Cheminformatics 2017 9:62

    Published on: 12 December 2017

  6. Research Article

    Consensus queries in ligand-based virtual screening experiments

    In ligand-based virtual screening experiments, a known active ligand is used in similarity searches to find putative active compounds for the same protein target. When there are several known active molecules,...

    Francois Berenger, Oanh Vu and Jens Meiler

    Journal of Cheminformatics 2017 9:60

    Published on: 28 November 2017

  7. Database

    The CompTox Chemistry Dashboard: a community data resource for environmental chemistry

    Despite an abundance of online databases providing access to chemical data, there is increasing demand for high-quality, structure-curated, open data to meet the various needs of the environmental sciences and co...

    Antony J. Williams, Christopher M. Grulke, Jeff Edwards, Andrew D. McEachran, Kamel Mansouri, Nancy C. Baker, Grace Patlewicz, Imran Shah, John F. Wambaugh, Richard S. Judson and Ann M. Richard

    Journal of Cheminformatics 2017 9:61

    Published on: 28 November 2017

  8. Research article

    Efficient conformational ensemble generation of protein-bound peptides

    Conformation generation of protein-bound peptides is critical for the determination of protein–peptide complex structures. Despite significant progress in conformer generation of small molecules, few methods h...

    Yumeng Yan, Di Zhang and Sheng-You Huang

    Journal of Cheminformatics 2017 9:59

    Published on: 22 November 2017

  9. Software

    eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations

    Computational methods to predict binding affinities of small ligands toward relevant biological (off-)targets are helpful in prioritizing the screening and synthesis of new drug candidates, thereby speeding up...

    Luigi Capoferri, Marc van Dijk, Ariën S. Rustenburg, Tsjerk A. Wassenaar, Derk P. Kooi, Eko A. Rifai, Nico P. E. Vermeulen and Daan P. Geerke

    Journal of Cheminformatics 2017 9:58

    Published on: 21 November 2017

  10. Research article

    An efficient computer-aided structural elucidation strategy for mixtures using an iterative dynamic programming algorithm

    The identification of chemical structures in natural product mixtures is an important task in drug discovery but is still a challenging problem, as structural elucidation is a time-consuming process and is li...

    Bo-Han Su, Meng-Yu Shen, Yeu-Chern Harn, San-Yuan Wang, Alioune Schurz, Chieh Lin, Olivia A. Lin and Yufeng J. Tseng

    Journal of Cheminformatics 2017 9:57

    Published on: 15 November 2017

  11. Research article

    A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD

    In order to make results of computational scientific research findable, accessible, interoperable and re-usable, it is necessary to decorate them with standardised metadata. However, there are a number of tech...

    Andrius Merkys, Nicolas Mounet, Andrea Cepellotti, Nicola Marzari, Saulius Gražulis and Giovanni Pizzi

    Journal of Cheminformatics 2017 9:56

    Published on: 14 November 2017

  12. Research article

    Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

    An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interact...

    Marcus D. Hanwell, Wibe A. de Jong and Christopher J. Harris

    Journal of Cheminformatics 2017 9:55

    Published on: 30 October 2017

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

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