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  1. Recent years have seen an explosion in the availability of data in the chemistry domain. With this information explosion, however, retrieving relevant results from the available information, and organising those ...

    Authors: Janna Hastings, Despoina Magka, Colin Batchelor, Lian Duan, Robert Stevens, Marcus Ennis and Christoph Steinbeck
    Citation: Journal of Cheminformatics 2012 4:8
  2. Analyzing chemical datasets is a challenging task for scientific researchers in the field of chemoinformatics. It is important, yet difficult to understand the relationship between the structure of chemical co...

    Authors: Martin Gütlein, Andreas Karwath and Stefan Kramer
    Citation: Journal of Cheminformatics 2012 4:7
  3. One of the largest challenges in chemistry today remains that of efficiently mining through vast amounts of data in order to elucidate the chemical structure for an unknown compound. The elucidated candidate c...

    Authors: Arvin Moser, Mikhail E Elyashberg, Antony J Williams, Kirill A Blinov and Joseph C DiMartino
    Citation: Journal of Cheminformatics 2012 4:5
  4. The current chemical space of known small molecules is estimated to exceed 1060 structures. Though the largest physical compound repositories contain only a few tens of millions of unique compounds, virtual scree...

    Authors: Narender Singh, Hongmao Sun, Sidhartha Chaudhury, Mohamed Diwan M AbdulHameed, Anders Wallqvist and Gregory Tawa
    Citation: Journal of Cheminformatics 2012 4:4
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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