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  1. Representations of chemical datasets in spreadsheet format are important for ready data assimilation and manipulation. In addition to the normal spreadsheet facilities, chemical spreadsheets need to have visua...

    Authors: Kevin R Lawson and Jonty Lawson

    Citation: Journal of Cheminformatics 2012 4:3

    Content type: Software

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  2. The mechanism of phospholipidosis is still not well understood. Numerous different mechanisms have been proposed, varying from direct inhibition of the breakdown of phospholipids to the binding of a drug compo...

    Authors: Robert Lowe, Hamse Y Mussa, Florian Nigsch, Robert C Glen and John BO Mitchell

    Citation: Journal of Cheminformatics 2012 4:2

    Content type: Research article

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  3. The use of SharePoint® collaboration software for content management has become a critical part of today's drug discovery process. SharePoint 2010 software has laid a foundation which enables researchers to colla...

    Authors: Kartik Tallapragada, Joseph Chewning, David Kombo and Beverly Ludwick

    Citation: Journal of Cheminformatics 2012 4:1

    Content type: Methodology

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  4. The computational processing and analysis of small molecules is at heart of cheminformatics and structural bioinformatics and their application in e.g. metabolomics or drug discovery. Pipelining or workflow to...

    Authors: Andreas Truszkowski, Kalai Vanii Jayaseelan, Stefan Neumann, Egon L Willighagen, Achim Zielesny and Christoph Steinbeck

    Citation: Journal of Cheminformatics 2011 3:54

    Content type: Software

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  5. In drug discovery, a positive Ames test for bacterial mutation presents a significant hurdle to advancing a drug to clinical trials. In a previous paper, we discussed success in predicting the genotoxicity of ...

    Authors: Patrick McCarren, Clayton Springer and Lewis Whitehead

    Citation: Journal of Cheminformatics 2011 3:51

    Content type: Research article

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  6. Quantitative structure-activity relationships (QSAR) analysis of peptides is helpful for designing various types of drugs such as kinase inhibitor or antigen. Capturing various properties of peptides is essent...

    Authors: Tsutomu Osoda and Satoru Miyano

    Citation: Journal of Cheminformatics 2011 3:50

    Content type: Research article

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  7. The articles in this special issue represent the culmination of about 15 years working with the potential of the web to support chemical and related subjects. The selection of papers arises from a symposium he...

    Authors: Peter Murray-Rust

    Citation: Journal of Cheminformatics 2011 3:48

    Content type: Editorial

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  8. The concept of Open Bibliography in science, technology and medicine (STM) is introduced as a combination of Open Source tools, Open specifications and Open bibliographic data. An Openly searchable and navigab...

    Authors: Richard Jones, Mark MacGillivray, Peter Murray-Rust, Jim Pitman, Peter Sefton, Ben O'Steen and William Waites

    Citation: Journal of Cheminformatics 2011 3:47

    Content type: Research article

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  9. The science journal is 346 years old in 2011, having evolved continuously but largely incrementally over that period. Its reinvention for an online presence has largely preserved its previously printed nature,...

    Authors: Henry S Rzepa

    Citation: Journal of Cheminformatics 2011 3:46

    Content type: Research article

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  10. The Ami project was a six month Rapid Innovation project sponsored by JISC to explore the Virtual Research Environment space. The project brainstormed with chemists and decided to investigate ways to facilitat...

    Authors: Brian J Brooks, Adam L Thorn, Matthew Smith, Peter Matthews, Shaoming Chen, Ben O'Steen, Sam E Adams, Joe A Townsend and Peter Murray-Rust

    Citation: Journal of Cheminformatics 2011 3:45

    Content type: Research article

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  11. A retrospective view of the design and evolution of Chemical Markup Language (CML) is presented by its original authors.

    Authors: Peter Murray-Rust and Henry S Rzepa

    Citation: Journal of Cheminformatics 2011 3:44

    Content type: Research article

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  12. The semantic architecture of CML consists of conventions, dictionaries and units. The conventions conform to a top-level specification and each convention can constrain compliant documents through machine-proc...

    Authors: Peter Murray-Rust, Joe A Townsend, Sam E Adams, Weerapong Phadungsukanan and Jens Thomas

    Citation: Journal of Cheminformatics 2011 3:43

    Content type: Research article

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  13. The World-Wide Molecular Matrix (WWMM) is a ten year project to create a peer-to-peer (P2P) system for the publication and collection of chemical objects, including over 250, 000 molecules. It has now been ins...

    Authors: Peter Murray-Rust, Sam E Adams, Jim Downing, Joe A Townsend and Yong Zhang

    Citation: Journal of Cheminformatics 2011 3:42

    Content type: Research article

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  14. The Open-Source Chemistry Analysis Routines (OSCAR) software, a toolkit for the recognition of named entities and data in chemistry publications, has been developed since 2002. Recent work has resulted in the ...

    Authors: David M Jessop, Sam E Adams, Egon L Willighagen, Lezan Hawizy and Peter Murray-Rust

    Citation: Journal of Cheminformatics 2011 3:41

    Content type: Software

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  15. Linked Open Data presents an opportunity to vastly improve the quality of science in all fields by increasing the availability and usability of the data upon which it is based. In the chemical field, there is ...

    Authors: David M Jessop, Sam E Adams and Peter Murray-Rust

    Citation: Journal of Cheminformatics 2011 3:40

    Content type: Research article

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  16. CMLLite is a collection of definitions and processes which provide strong and flexible validation for a document in Chemical Markup Language (CML). It consists of an updated CML schema (schema3), conventions s...

    Authors: Joe A Townsend and Peter Murray-Rust

    Citation: Journal of Cheminformatics 2011 3:39

    Content type: Research article

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  17. Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of...

    Authors: Sam Adams, Pablo de Castro, Pablo Echenique, Jorge Estrada, Marcus D Hanwell, Peter Murray-Rust, Paul Sherwood, Jens Thomas and Joe Townsend

    Citation: Journal of Cheminformatics 2011 3:38

    Content type: Research article

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  18. The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by prom...

    Authors: Noel M O'Boyle, Rajarshi Guha, Egon L Willighagen, Samuel E Adams, Jonathan Alvarsson, Jean-Claude Bradley, Igor V Filippov, Robert M Hanson, Marcus D Hanwell, Geoffrey R Hutchison, Craig A James, Nina Jeliazkova, Andrew SID Lang, Karol M Langner, David C Lonie, Daniel M Lowe…

    Citation: Journal of Cheminformatics 2011 3:37

    Content type: Research article

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  19. The advent of open access to peer reviewed scholarly literature in the biomedical sciences creates the opening to examine scholarship in general, and chemistry in particular, to see where and how novel forms o...

    Authors: John Wilbanks

    Citation: Journal of Cheminformatics 2011 3:36

    Content type: Commentary

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  20. This article contains the slides and transcript of a talk given by Dan Zaharevitz at the "Visions of a Semantic Molecular Future" symposium held at the University of Cambridge Department of Chemistry on 2011-0...

    Authors: Dan W Zaharevitz

    Citation: Journal of Cheminformatics 2011 3:34

    Content type: Oral presentation

    Published on:

  21. A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto ...

    Authors: Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch and Geoffrey R Hutchison

    Citation: Journal of Cheminformatics 2011 3:33

    Content type: Software

    Published on:

  22. PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an eff...

    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

    Content type: Software

    Published on:

  23. 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

    Content type: Preliminary communication

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  24. Data fusion methods are widely used in virtual screening, and make the implicit assumption that the more often a molecule is retrieved in multiple similarity searches, the more likely it is to be active. This ...

    Authors: John D Holliday, Evangelos Kanoulas, Nurul Malim and Peter Willett

    Citation: Journal of Cheminformatics 2011 3:29

    Content type: Research article

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  25. Machine learning has a vast range of applications. In particular, advanced machine learning methods are routinely and increasingly used in quantitative structure activity relationship (QSAR) modeling. QSAR dat...

    Authors: Jonna C Stålring, Lars A Carlsson, Pedro Almeida and Scott Boyer

    Citation: Journal of Cheminformatics 2011 3:28

    Content type: Software

    Published on:

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

    Authors: Jochen Junker

    Citation: Journal of Cheminformatics 2011 3:27

    Content type: Preliminary communication

    Published on:

  27. 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 se...

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

    Citation: Journal of Cheminformatics 2011 3:26

    Content type: Research article

    Published on:

  28. 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

    Content type: Review

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  29. The performance of 3D-based virtual screening similarity functions is affected by the applied conformations of compounds. Therefore, the results of 3D approaches are often less robust than 2D approaches. The a...

    Authors: Andreas Jahn, Lars Rosenbaum, Georg Hinselmann and Andreas Zell

    Citation: Journal of Cheminformatics 2011 3:23

    Content type: Research article

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  30. Over the past several centuries, chemistry has permeated virtually every facet of human lifestyle, enriching fields as diverse as medicine, agriculture, manufacturing, warfare, and electronics, among numerous ...

    Authors: Leonid L Chepelev and Michel Dumontier

    Citation: Journal of Cheminformatics 2011 3:20

    Content type: Methodology

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  31. There is an abundance of information about drugs available on the Web. Data sources range from medicinal chemistry results, over the impact of drugs on gene expression, to the outcomes of drugs in clinical tri...

    Authors: Matthias Samwald, Anja Jentzsch, Christopher Bouton, Claus Stie Kallesøe, Egon Willighagen, Janos Hajagos, M Scott Marshall, Eric Prud'hommeaux, Oktie Hassanzadeh, Elgar Pichler and Susie Stephens

    Citation: Journal of Cheminformatics 2011 3:19

    Content type: Preliminary communication

    Published on:

  32. The primary method for scientific communication is in the form of published scientific articles and theses which use natural language combined with domain-specific terminology. As such, they contain free owing...

    Authors: Lezan Hawizy, David M Jessop, Nico Adams and Peter Murray-Rust

    Citation: Journal of Cheminformatics 2011 3:17

    Content type: Research article

    Published on:

  33. Since the classic Hopkins and Groom druggable genome review in 2002, there have been a number of publications updating both the hypothetical and successful human drug target statistics. However, listings of re...

    Authors: Christopher Southan, Kiran Boppana, Sarma ARP Jagarlapudi and Sorel Muresan

    Citation: Journal of Cheminformatics 2011 3:14

    Content type: Research article

    Published on:

  34. PubChem is a free and open public resource for the biological activities of small molecules. With many tens of millions of both chemical structures and biological test results, PubChem is a sizeable system wit...

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

    Citation: Journal of Cheminformatics 2011 3:13

    Content type: Research article

    Published on:

  35. Virtual (computational) screening is an increasingly important tool for drug discovery. AutoDock is a popular open-source application for performing molecular docking, the prediction of ligand-receptor interac...

    Authors: Andrew P Norgan, Paul K Coffman, Jean-Pierre A Kocher, David J Katzmann and Carlos P Sosa

    Citation: Journal of Cheminformatics 2011 3:12

    Content type: Software

    Published on:

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