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  1. Content type: Research article

    The collection of chemical structure information and associated experimental data for quantitative structure–activity/property relationship (QSAR/QSPR) modeling is facilitated by an increasing number of public...

    Authors: Kamel Mansouri, Chris M. Grulke, Richard S. Judson and Antony J. Williams

    Citation: Journal of Cheminformatics 2018 10:10

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  2. Content type: Research article

    Spectrophores are novel descriptors that are calculated from the three-dimensional atomic properties of molecules. In our current implementation, the atomic properties that were used to calculate spectrophores...

    Authors: Rafaela Gladysz, Fabio Mendes Dos Santos, Wilfried Langenaeker, Gert Thijs, Koen Augustyns and Hans De Winter

    Citation: Journal of Cheminformatics 2018 10:9

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  3. Content type: Methodology

    Docking and scoring large libraries of ligands against target proteins forms the basis of structure-based virtual screening. The problem is trivially parallelizable, and calculations are generally carried out ...

    Authors: Laeeq Ahmed, Valentin Georgiev, Marco Capuccini, Salman Toor, Wesley Schaal, Erwin Laure and Ola Spjuth

    Citation: Journal of Cheminformatics 2018 10:8

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  4. Content type: Research article

    Iterative screening has emerged as a promising approach to increase the efficiency of screening campaigns compared to traditional high throughput approaches. By learning from a subset of the compound library, ...

    Authors: Fredrik Svensson, Avid M. Afzal, Ulf Norinder and Andreas Bender

    Citation: Journal of Cheminformatics 2018 10:7

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  5. Content type: Research article

    Given that many antifungal medications are susceptible to evolved resistance, there is a need for novel drugs with unique mechanisms of action. Inhibiting the essential proton pump Pma1p, a P-type ATPase, is a...

    Authors: Sabine Ottilie, Gregory M. Goldgof, Andrea L. Cheung, Jennifer L. Walker, Edgar Vigil, Kenneth E. Allen, Yevgeniya Antonova-Koch, Carolyn W. Slayman, Yo Suzuki and Jacob D. Durrant

    Citation: Journal of Cheminformatics 2018 10:6

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  6. Content type: Review

    OriginLab’s newest version update to Origin and OriginPro includes ease-of-use features, like Origin Central updates and creation of an App Center, as well as larger changes like the addition of Unicode charac...

    Authors: James G. Moberly, Matthew T. Bernards and Kristopher V. Waynant

    Citation: Journal of Cheminformatics 2018 10:5

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  7. Content type: Software

    Molecular descriptors are widely employed to present molecular characteristics in cheminformatics. Various molecular-descriptor-calculation software programs have been developed. However, users of those progra...

    Authors: Hirotomo Moriwaki, Yu-Shi Tian, Norihito Kawashita and Tatsuya Takagi

    Citation: Journal of Cheminformatics 2018 10:4

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  8. Content type: Research article

    Idiosyncratic adverse drug reactions have been linked to a drug’s ability to bind with a human leukocyte antigen (HLA) protein. However, due to the thousands of HLA variants and limited structural data for dru...

    Authors: George Van Den Driessche and Denis Fourches

    Citation: Journal of Cheminformatics 2018 10:3

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  9. Content type: Research article

    Aromatase is a member of the cytochrome P450 superfamily responsible for a key step in the biosynthesis of estrogens. As estrogens are involved in the control of important reproduction-related processes, inclu...

    Authors: Sehan Lee and Mace G. Barron

    Citation: Journal of Cheminformatics 2018 10:2

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  10. Content type: Research article

    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...

    Authors: Samina Kausar and Andre O. Falcao

    Citation: Journal of Cheminformatics 2018 10:1

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  11. Content type: Research article

    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 ...

    Authors: 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

    Citation: Journal of Cheminformatics 2017 9:67

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  12. Content type: Methodology

    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...

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

    Citation: Journal of Cheminformatics 2017 9:65

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  13. Content type: Research article

    Deciphering the structural determinants of protein–protein interactions (PPIs) is essential to gain a deep understanding of many important biological functions in the living cells. Computational approaches for...

    Authors: Ting Feng, Fu Chen, Yu Kang, Huiyong Sun, Hui Liu, Dan Li, Feng Zhu and Tingjun Hou

    Citation: Journal of Cheminformatics 2017 9:66

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  14. Content type: Methodology

    Network generation tools coupled with chemical reaction rules have been mainly developed for synthesis planning and more recently for metabolic engineering. Using the same core algorithm, these tools apply a s...

    Authors: Mathilde Koch, Thomas Duigou, Pablo Carbonell and Jean-Loup Faulon

    Citation: Journal of Cheminformatics 2017 9:64

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  15. Content type: Research article

    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...

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

    Citation: Journal of Cheminformatics 2017 9:63

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  16. Content type: Software

    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...

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

    Citation: Journal of Cheminformatics 2017 9:62

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  17. Content type: Research Article

    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,...

    Authors: Francois Berenger, Oanh Vu and Jens Meiler

    Citation: Journal of Cheminformatics 2017 9:60

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  18. Content type: Database

    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...

    Authors: 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

    Citation: Journal of Cheminformatics 2017 9:61

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  19. Content type: Software

    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...

    Authors: 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

    Citation: Journal of Cheminformatics 2017 9:58

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  20. Content type: Research article

    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...

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

    Citation: Journal of Cheminformatics 2017 9:57

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  21. Content type: Research article

    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...

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

    Citation: Journal of Cheminformatics 2017 9:56

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  22. Content type: Software

    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 ...

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

    Citation: Journal of Cheminformatics 2017 9:54

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  23. Content type: Erratum

    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 9:53

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

  24. Content type: Software

    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...

    Authors: Patrick Ropp, Aaron Friedman and Jacob D. Durrant

    Citation: Journal of Cheminformatics 2017 9:52

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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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

  37. 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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  38. 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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  39. 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

  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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