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  1. Content type: Research article

    In drug design, one may be confronted to the problem of finding hits for targets for which no small inhibiting molecules are known and only low-throughput experiments are available (like ITC or NMR studies), t...

    Authors: Ludovic Chaput, Juan Martinez-Sanz, Eric Quiniou, Pascal Rigolet, Nicolas Saettel and Liliane Mouawad

    Citation: Journal of Cheminformatics 2016 8:1

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  2. Content type: Research article

    A number of algorithms have been proposed to predict the biological targets of diverse molecules. Some are structure-based, but the most common are ligand-based and use chemical fingerprints and the notion of...

    Authors: Alessandro Lusci, David Fooshee, Michael Browning, Joshua Swamidass and Pierre Baldi

    Citation: Journal of Cheminformatics 2015 7:63

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  3. Content type: Software

    Molecular descriptors and fingerprints have been routinely used in QSAR/SAR analysis, virtual drug screening, compound search/ranking, drug ADME/T prediction and other drug discovery processes. Since the calc...

    Authors: Jie Dong, Dong-Sheng Cao, Hong-Yu Miao, Shao Liu, Bai-Chuan Deng, Yong-Huan Yun, Ning-Ning Wang, Ai-Ping Lu, Wen-Bin Zeng and Alex F. Chen

    Citation: Journal of Cheminformatics 2015 7:60

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  4. Content type: Research article

    Partial atomic charges describe the distribution of electron density in a molecule and therefore provide clues to the chemical behaviour of molecules. Recently, these charges have become popular in chemoinform...

    Authors: Stanislav Geidl, Tomáš Bouchal, Tomáš Raček, Radka Svobodová Vařeková, Václav Hejret, Aleš Křenek, Ruben Abagyan and Jaroslav Koča

    Citation: Journal of Cheminformatics 2015 7:59

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  5. Content type: Commentary

    It is common in cheminformatics to represent the properties of a ligand as a string of 1’s and 0’s, with the intention of elucidating, inter alia, the relationship between the chemical structure of a ligand and i...

    Authors: Hamse Y. Mussa, John B. O. Mitchell and Robert C. Glen

    Citation: Journal of Cheminformatics 2015 7:58

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  6. Content type: Research article

    The formation of intramolecular hydrogen bonds (IHBs) may induce the remarkable changes in molecular physicochemical properties. Within the framework of the extended solvent-contact model, we investigate the e...

    Authors: Kee-Choo Chung and Hwangseo Park

    Citation: Journal of Cheminformatics 2015 7:57

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  7. Content type: Research article

    The enriched biological activity information of compounds in large and freely-accessible chemical databases like the PubChem Bioassay Database has become a powerful research resource for the scientific researc...

    Authors: Xiang Yu, Lewis Y. Geer, Lianyi Han and Stephen H. Bryant

    Citation: Journal of Cheminformatics 2015 7:55

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  8. Content type: Research article

    A wide range of chemical compound databases are currently available for pharmaceutical research. To retrieve compound information, including structures, researchers can query these chemical databases using non...

    Authors: Saber A. Akhondi, Sorel Muresan, Antony J. Williams and Jan A. Kors

    Citation: Journal of Cheminformatics 2015 7:54

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  9. Content type: Research article

    A new lipid class named ‘fatty acid esters of hydroxyl fatty acids’ (FAHFA) was recently discovered in mammalian adipose tissue and in blood plasma and some FAHFAs were found to be associated with type 2 diabe...

    Authors: Yan Ma, Tobias Kind, Arpana Vaniya, Ingrid Gennity, Johannes F. Fahrmann and Oliver Fiehn

    Citation: Journal of Cheminformatics 2015 7:53

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  10. Content type: Research article

    In the present work, we aim to transfer to the field of virtual screening the predictiveness curve, a metric that has been advocated in clinical epidemiology. The literature describes the use of predictiveness...

    Authors: Charly Empereur-mot, Hélène Guillemain, Aurélien Latouche, Jean-François Zagury, Vivian Viallon and Matthieu Montes

    Citation: Journal of Cheminformatics 2015 7:52

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  11. Content type: Research article

    In silico analyses are increasingly being used to support mode-of-action investigations; however many such approaches do not utilise the large amounts of inactive data held in chemogenomic repositories. The ob...

    Authors: Lewis H. Mervin, Avid M. Afzal, Georgios Drakakis, Richard Lewis, Ola Engkvist and Andreas Bender

    Citation: Journal of Cheminformatics 2015 7:51

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  12. Content type: Software

    Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites.

    Authors: Crina-Maria Ionescu, David Sehnal, Francesco L. Falginella, Purbaj Pant, Lukáš Pravda, Tomáš Bouchal, Radka Svobodová Vařeková, Stanislav Geidl and Jaroslav Koča

    Citation: Journal of Cheminformatics 2015 7:50

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  13. Content type: Research article

    First public disclosure of new chemical entities often takes place in patents, which makes them an important source of information. However, with an ever increasing number of patent applications, manual proces...

    Authors: Stefan Senger, Luca Bartek, George Papadatos and Anna Gaulton

    Citation: Journal of Cheminformatics 2015 7:49

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  14. Content type: Review

    Enzymes are one of the most important groups of drug targets, and identifying possible ligand-enzyme interactions is of major importance in many drug discovery processes. Novel computational methods have been ...

    Authors: Janez Konc, Samo Lešnik and Dušanka Janežič

    Citation: Journal of Cheminformatics 2015 7:48

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  15. Content type: Software

    The interaction of a small molecule with a protein target depends on its ability to adopt a three-dimensional structure that is complementary. Therefore, complete and rapid prediction of the conformational spa...

    Authors: Sandeepkumar Kothiwale, Jeffrey L. Mendenhall and Jens Meiler

    Citation: Journal of Cheminformatics 2015 7:47

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  16. Content type: Research article

    Predictive regression models can be created with many different modelling approaches. Choices need to be made for data set splitting, cross-validation methods, specific regression parameters and best model cr...

    Authors: Georgia Tsiliki, Cristian R. Munteanu, Jose A. Seoane, Carlos Fernandez-Lozano, Haralambos Sarimveis and Egon L. Willighagen

    Citation: Journal of Cheminformatics 2015 7:46

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  17. Content type: Software

    In silico predictive models have proved to be valuable for the optimisation of compound potency, selectivity and safety profiles in the drug discovery process.

    Authors: Daniel S Murrell, Isidro Cortes-Ciriano, Gerard J P van Westen, Ian P Stott, Andreas Bender, Thérèse E Malliavin and Robert C Glen

    Citation: Journal of Cheminformatics 2015 7:45

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  18. Content type: Database

    In spite of its great promise, metabolomics has proven difficult to execute in an untargeted and generalizable manner. Liquid chromatography–mass spectrometry (LC–MS) has made it possible to gather data on tho...

    Authors: James G Jeffryes, Ricardo L Colastani, Mona Elbadawi-Sidhu, Tobias Kind, Thomas D Niehaus, Linda J Broadbelt, Andrew D Hanson, Oliver Fiehn, Keith E J Tyo and Christopher S Henry

    Citation: Journal of Cheminformatics 2015 7:44

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  19. Content type: Research article

    The desirable curation of 158,122 molecular geometries derived from the NCI set of reference molecules together with associated properties computed using the MOPAC semi-empirical quantum mechanical method and ...

    Authors: Matthew J Harvey, Nicholas J Mason, Andrew McLean, Peter Murray-Rust, Henry S Rzepa and James J P Stewart

    Citation: Journal of Cheminformatics 2015 7:43

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  20. Content type: Research article

    With the rapid increase of the structural data of biomolecular complexes, novel structural analysis methods have to be devised with high-throughput capacity to handle immense data input and to construct massiv...

    Authors: Mohammad ElGamacy and Luc Van Meervelt

    Citation: Journal of Cheminformatics 2015 7:42

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  21. Content type: Research article

    Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure se...

    Authors: Volker D Hähnke, Evan E Bolton and Stephen H Bryant

    Citation: Journal of Cheminformatics 2015 7:41

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  22. Content type: Software

    The design of QSAR/QSPR models is a challenging problem, where the selection of the most relevant descriptors constitutes a key step of the process. Several feature selection methods that address this step are...

    Authors: María Jimena Martínez, Ignacio Ponzoni, Mónica F Díaz, Gustavo E Vazquez and Axel J Soto

    Citation: Journal of Cheminformatics 2015 7:39

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  23. Content type: Research article

    Support Vector Machine has become one of the most popular machine learning tools used in virtual screening campaigns aimed at finding new drug candidates. Although it can be extremely effective in finding new ...

    Authors: Wojciech M Czarnecki, Sabina Podlewska and Andrzej J Bojarski

    Citation: Journal of Cheminformatics 2015 7:38

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  24. Content type: Research article

    We describe three different procedures based on metadata standards for enabling automated retrieval of scientific data from digital repositories utilising the persistent identifier of the dataset with optional...

    Authors: Matthew J Harvey, Nicholas J Mason, Andrew McLean and Henry S Rzepa

    Citation: Journal of Cheminformatics 2015 7:37

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  25. Content type: Database

    PubChem is an open repository for chemical structures, biological activities and biomedical annotations. Semantic Web technologies are emerging as an increasingly important approach to distribute and integrate...

    Authors: Gang Fu, Colin Batchelor, Michel Dumontier, Janna Hastings, Egon Willighagen and Evan Bolton

    Citation: Journal of Cheminformatics 2015 7:34

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  26. Content type: Research article

    Developing structure–activity relationships (SARs) of molecules is an important approach in facilitating hit exploration in the early stage of drug discovery. Although information on millions of compounds and ...

    Authors: Sunghwan Kim, Lianyi Han, Bo Yu, Volker D Hähnke, Evan E Bolton and Stephen H Bryant

    Citation: Journal of Cheminformatics 2015 7:33

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  27. Content type: Database

    Both metabolism and transport are key elements defining the bioavailability and biological activity of molecules, i.e. their adverse and therapeutic effects. Structured and high quality experimental data store...

    Authors: Lora Mak, David Marcus, Andrew Howlett, Galina Yarova, Guus Duchateau, Werner Klaffke, Andreas Bender and Robert C Glen

    Citation: Journal of Cheminformatics 2015 7:31

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  28. Content type: Methodology

    There are presently hundreds of online databases hosting millions of chemical compounds and associated data. As a result of the number of cheminformatics software tools that can be used to produce the data, su...

    Authors: Karen Karapetyan, Colin Batchelor, David Sharpe, Valery Tkachenko and Antony J Williams

    Citation: Journal of Cheminformatics 2015 7:30

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  29. Content type: Database

    Natural products (NPs) are important to the drug discovery process. NP research efforts are expanding world-wide and South Africa is no exception to this. While freely-accessible small molecule databases, cont...

    Authors: Rowan Hatherley, David K Brown, Thommas M Musyoka, David L Penkler, Ngonidzashe Faya, Kevin A Lobb and Özlem Tastan Bishop

    Citation: Journal of Cheminformatics 2015 7:29

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  30. Content type: Software

    The increased use of small-molecule compound screening by new users from a variety of different academic backgrounds calls for adequate software to administer, appraise, analyse and exchange information obtain...

    Authors: Parisa Amani, Todd Sneyd, Sarah Preston, Neil D Young, Lyndel Mason, Ulla-Maja Bailey, Jonathan Baell, David Camp, Robin B Gasser, Alain-Dominique Gorse, Paul Taylor and Andreas Hofmann

    Citation: Journal of Cheminformatics 2015 7:28

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  31. Content type: Research article

    In a recent paper, Mussa, Mitchell and Glen (MMG) have mathematically demonstrated that the “Laplacian Corrected Modified Naïve Bayes” (LCMNB) algorithm can be viewed as a variant of the so-called Standard Na...

    Authors: Hamse Y Mussa, David Marcus, John B O Mitchell and Robert C Glen

    Citation: Journal of Cheminformatics 2015 7:27

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  32. Content type: Research article

    According to Cobanoglu et al., it is now widely acknowledged that the single target paradigm (one protein/target, one disease, one drug) that has been the dominant premise in drug development in the recent pas...

    Authors: Avid M Afzal, Hamse Y Mussa, Richard E Turner, Andreas Bender and Robert C Glen

    Citation: Journal of Cheminformatics 2015 7:24

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  33. Content type: Research article

    This paper documents the design, layout and algorithms of the IUPAC International Chemical Identifier, InChI.

    Authors: Stephen R Heller, Alan McNaught, Igor Pletnev, Stephen Stein and Dmitrii Tchekhovskoi

    Citation: Journal of Cheminformatics 2015 7:23

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  34. Content type: Research article

    Structure-based virtual screening techniques can help to identify new lead structures and complement other screening approaches in drug discovery. Prior to docking, the data (protein crystal structures and lig...

    Authors: Tamer M Ibrahim, Matthias R Bauer and Frank M Boeckler

    Citation: Journal of Cheminformatics 2015 7:21

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  35. Content type: Research article

    Quantitative description of dose–response of a drug for complex systems is essential for treatment of diseases and drug discovery. Given the growth of large-scale biological data obtained by multi-level assays...

    Authors: Jiangyong Gu, Xinzhuang Zhang, Yimin Ma, Na Li, Fang Luo, Liang Cao, Zhenzhong Wang, Gu Yuan, Lirong Chen, Wei Xiao and Xiaojie Xu

    Citation: Journal of Cheminformatics 2015 7:19

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  36. Content type: Methodology

    Computational approaches have emerged as an instrumental methodology in modern research. For example, virtual screening by molecular docking is routinely used in computer-aided drug discovery. One of the criti...

    Authors: Wei P. Feinstein and Michal Brylinski

    Citation: Journal of Cheminformatics 2015 7:18

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  37. Content type: Software

    Spectra visualisation from methods such as mass spectroscopy, infrared spectroscopy or nuclear magnetic resonance is an essential part of every web-facing spectral resource. The development of an intuitive and...

    Authors: Stephan Beisken, Pablo Conesa, Kenneth Haug, Reza M Salek and Christoph Steinbeck

    Citation: Journal of Cheminformatics 2015 7:17

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  38. Content type: Software

    The novel program for graphical display and editing of molecular systems, luscus, is described. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of ...

    Authors: Goran Kovačević and Valera Veryazov

    Citation: Journal of Cheminformatics 2015 7:16

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