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220 result(s) for 'PubChem' within Journal of Cheminformatics

Page 1 of 5

  1. Content type: Database

    PubChem is an open archive consisting of a ... . Currently (as of Nov. 2015), PubChem contains more than 150 million depositor-provided...

    Authors: Sunghwan Kim, Paul A. Thiessen, Tiejun Cheng, Bo Yu, Benjamin A. Shoemaker, Jiyao Wang, Evan E. Bolton, Yanli Wang and Stephen H. Bryant

    Citation: Journal of Cheminformatics 2016 8:32

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  2. Content type: Software

    PubChem is an important public, Web-based information ... JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence...

    Authors: Wolf D Ihlenfeldt, Evan E Bolton and Stephen H Bryant

    Citation: Journal of Cheminformatics 2009 1:20

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  3. Content type: Research article

    PubChem is a chemical information repository, consisting of ... structure standardization. The present study describes the PubChem standardization approaches and analyzes them for their ... structures during the ...

    Authors: Volker D. Hähnke, Sunghwan Kim and Evan E. Bolton

    Citation: Journal of Cheminformatics 2018 10:36

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  4. Content type: Research article

    PubChem is a public repository for biological activities ... of its vast amount of chemical information, PubChem performs 2-dimensional (2-D) and ... precompute “neighbor” relationships between molecules in the PubChem

    Authors: Sunghwan Kim, Evan E. Bolton and Stephen H. Bryant

    Citation: Journal of Cheminformatics 2016 8:62

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  5. Content type: Research article

    For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. B...

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

    Citation: Journal of Cheminformatics 2015 7:41

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  6. Content type: Database

    PubChem is a chemical data repository that provides ... with new opportunities for data-intensive research. PubChem provides several programmatic access routes. One of ... interface specialized for accessing anno...

    Authors: Sunghwan Kim, Paul A. Thiessen, Tiejun Cheng, Jian Zhang, Asta Gindulyte and Evan E. Bolton

    Citation: Journal of Cheminformatics 2019 11:56

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  7. Content type: Research article

    Research discussed in the present paper employed a bioactivity-centered clustering approach to group 843,845 non-inactive compounds stored in PubChem according to both structural similarity and bioactivity ... wi...

    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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  8. Content type: Software

    PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, ... with similar biological efficacies against targe...

    Authors: Evan E Bolton, Jie Chen, Sunghwan Kim, Lianyi Han, Siqian He, Wenyao Shi, Vahan Simonyan, Yan Sun, Paul A Thiessen, Jiyao Wang, Bo Yu, Jian Zhang and Stephen H Bryant

    Citation: Journal of Cheminformatics 2011 3:32

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  9. Content type: Research article

    Where they could be calculated, extracted compounds-per-journal article were in the range of 12 to 19 but compound-per-protein counts increased with document numbers. Chemical structure filtration to facilitate s...

    Authors: Christopher Southan, Péter Várkonyi and Sorel Muresan

    Citation: Journal of Cheminformatics 2009 1:10

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  10. Content type: Research article

    The use of 3-D similarity techniques in the analysis of biological data and virtual screening is pervasive, but what is a biologically meaningful 3-D similarity value? Can one find statistically significant separ...

    Authors: Sunghwan Kim, Evan E Bolton and Stephen H Bryant

    Citation: Journal of Cheminformatics 2011 3:26

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  11. Content type: Research article

    PubChem is a free and open public resource ... both chemical structures and biological test results, PubChem is a sizeable system with an uneven ... of available information. Some chemical structures in PubChem i...

    Authors: Evan E Bolton, Sunghwan Kim and Stephen H Bryant

    Citation: Journal of Cheminformatics 2011 3:13

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  12. Content type: Research article

    PubChem is a free and publicly available resource ... activity information. PubChem3D is an extension to PubChem containing computationally-derived three-dimensional (3-D...

    Authors: Sunghwan Kim, Evan E Bolton and Stephen H Bryant

    Citation: Journal of Cheminformatics 2013 5:1

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  13. Content type: Software

    MetFrag has gone through algorithmic and scoring refinements. New features include the retrieval of reference, data source and patent information via ChemSpider and PubChem web services, as well as InChIKey filte...

    Authors: Christoph Ruttkies, Emma L. Schymanski, Sebastian Wolf, Juliane Hollender and Steffen Neumann

    Citation: Journal of Cheminformatics 2016 8:3

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  14. Content type: Research article

    An important step in the reconstruction of a metabolic network is annotation of metabolites. Metabolites are generally annotated with various database or structure based identifiers. Metabolite annotations in ...

    Authors: Hulda S Haraldsdóttir, Ines Thiele and Ronan MT Fleming

    Citation: Journal of Cheminformatics 2014 6:2

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  15. Content type: Software

    In recent years, there has been a huge increase in the amount of publicly-available and proprietary information pertinent to drug discovery. However, there is a distinct lack of data mining tools available to ...

    Authors: Qian Zhu, Michael S Lajiness, Ying Ding and David J Wild

    Citation: Journal of Cheminformatics 2010 2:6

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  16. Content type: Research

    Our system uses a mixture of expertly curated grammars and dictionaries, as well as dictionaries automatically derived from public resources. We show that the heuristics developed to filter our dictionary of triv...

    Authors: Daniel M Lowe and Roger A Sayle

    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S5

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    This article is part of a Supplement: Volume 7 Supplement 1

  17. Content type: Research article

    The properties of fragrance molecules in the public databases SuperScent and Flavornet were analyzed to define a “fragrance-like” (FL) property range (Heavy Atom Count ≤ 21, only C, H, O, S, (O + S) ≤ 3, Hydrogen...

    Authors: Lars Ruddigkeit, Mahendra Awale and Jean-Louis Reymond

    Citation: Journal of Cheminformatics 2014 6:27

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  18. Content type: Research article

    The shape diversity of 16.4 million biologically relevant molecules from the PubChem Compound database and their 1.46 billion...

    Authors: Evan E Bolton, Sunghwan Kim and Stephen H Bryant

    Citation: Journal of Cheminformatics 2011 3:9

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  19. 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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  20. Content type: Database

    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. T...

    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 9:17

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    The Erratum to this article has been published in Journal of Cheminformatics 2017 9:41

  21. Content type: Research article

    This study aims at improving upon existing activity predictions methods by augmenting chemical structure fingerprints with bio-activity based fingerprints derived from high-throughput screening (HTS) data (HTSFPs...

    Authors: Oliver Laufkötter, Noé Sturm, Jürgen Bajorath, Hongming Chen and Ola Engkvist

    Citation: Journal of Cheminformatics 2019 11:54

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  22. 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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  23. Content type: Research article

    Proteinogenic and non-proteinogenic amino acids, fatty acids or glycans are some of the main building blocks of nonribsosomal peptides (NRPs) and as such may give insight into the origin, biosynthesis and bioacti...

    Authors: Emma Ricart, Valérie Leclère, Areski Flissi, Markus Mueller, Maude Pupin and Frédérique Lisacek

    Citation: Journal of Cheminformatics 2019 11:13

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  24. 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 objec...

    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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  25. Content type: Database

    Here we present Metabolic In silico Network Expansions (MINEs), an extension of known metabolite databases to include molecules that have not been observed, but are likely to occur based on known metabolites and ...

    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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  26. Content type: Preliminary communication

    Herein is proposed a general approach to represent an entire compound library with a single binary fingerprint. The development of the database fingerprint (DFP) is illustrated first using a short fingerprint (MA...

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

    Citation: Journal of Cheminformatics 2017 9:9

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  27. Content type: Research

    The past decade has seen an upsurge in the number of publications in chemistry. The ever-swelling volume of available documents makes it increasingly hard to extract relevant new information from such unstruct...

    Authors: Saber A Akhondi, Kristina M Hettne, Eelke van der Horst, Erik M van Mulligen and Jan A Kors

    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S10

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    This article is part of a Supplement: Volume 7 Supplement 1

  28. Content type: Research article

    Pharmaceutical bioassay data is not readily available to the academic community. The data held at PubChem is not curated and there is a...

    Authors: Amanda C Schierz

    Citation: Journal of Cheminformatics 2009 1:21

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  29. Content type: Software

    Scientists have long been driven by the desire to describe, organize, classify, and compare objects using taxonomies and/or ontologies. In contrast to biology, geology, and many other scientific disciplines, t...

    Authors: Yannick Djoumbou Feunang, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner and David S. Wishart

    Citation: Journal of Cheminformatics 2016 8:61

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  30. Content type: Research Article

    Untargeted metabolomics commonly uses liquid chromatography mass spectrometry to measure abundances of metabolites; subsequent tandem mass spectrometry is used to derive information about individual compounds....

    Authors: Sebastian Böcker and Kai Dührkop

    Citation: Journal of Cheminformatics 2016 8:5

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  31. Content type: Research article

    The method for estimation of the synthetic accessibility score (SAscore) described here is based on a combination of fragment contributions and a complexity penalty. Fragment contributions have been calculated ba...

    Authors: Peter Ertl and Ansgar Schuffenhauer

    Citation: Journal of Cheminformatics 2009 1:8

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  32. Content type: Preliminary communication

    The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The difficulty of a structure elucidation problem depends more on the typ...

    Authors: Jochen Junker

    Citation: Journal of Cheminformatics 2011 3:31

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  33. Content type: Review

    Due to recent advances in data storage and sharing for further data processing in predictive toxicology, there is an increasing need for flexible data representations, secure and consistent data curation and a...

    Authors: Xin Fu, Anna Wojak, Daniel Neagu, Mick Ridley and Kim Travis

    Citation: Journal of Cheminformatics 2011 3:24

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  34. Content type: Research article

    A new algorithm has been developed to enable the interpretation of black box models. The developed algorithm is agnostic to learning algorithm and open to all structural based descriptors such as fragments, ke...

    Authors: Samuel J Webb, Thierry Hanser, Brendan Howlin, Paul Krause and Jonathan D Vessey

    Citation: Journal of Cheminformatics 2014 6:8

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