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  1. Previously, we developed a combined dictionary dubbed Chemlist for the identification of small molecules and drugs in text based on a number of publicly available databases and tested it on an annotated corpus...

    Authors: Kristina M Hettne, Antony J Williams, Erik M van Mulligen, Jos Kleinjans, Valery Tkachenko and Jan A Kors

    Citation: Journal of Cheminformatics 2010 2:3

    Content type: Research article

    Published on:

  2. The virtual screening of large compound databases is an important application of structural-activity relationship models. Due to the high structural diversity of these data sets, it is impossible for machine l...

    Authors: Nikolas Fechner, Andreas Jahn, Georg Hinselmann and Andreas Zell

    Citation: Journal of Cheminformatics 2010 2:2

    Content type: Research article

    Published on:

  3. A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editor...

    Authors: Peter Ertl

    Citation: Journal of Cheminformatics 2010 2:1

    Content type: Review

    Published on:

  4. There are three main problems associated with the virtual screening of bioassay data. The first is access to freely-available curated data, the second is the number of false positives that occur in the physica...

    Authors: Amanda C Schierz

    Citation: Journal of Cheminformatics 2009 1:21

    Content type: Research article

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  5. PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandator...

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

    Citation: Journal of Cheminformatics 2009 1:20

    Content type: Software

    Published on:

  6. The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognit...

    Authors: Vishwesh Venkatraman, Padmasini Ramji Chakravarthy and Daisuke Kihara

    Citation: Journal of Cheminformatics 2009 1:19

    Content type: Research article

    Published on:

  7. Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engine...

    Authors: Mark Rijnbeek and Christoph Steinbeck

    Citation: Journal of Cheminformatics 2009 1:17

    Content type: Software

    Published on:

  8. Ligand-based virtual screening experiments are an important task in the early drug discovery stage. An ambitious aim in each experiment is to disclose active structures based on new scaffolds. To perform these...

    Authors: Andreas Jahn, Georg Hinselmann, Nikolas Fechner and Andreas Zell

    Citation: Journal of Cheminformatics 2009 1:14

    Content type: Research article

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  9. Finding one small molecule (query) in a large target library is a challenging task in computational chemistry. Although several heuristic approaches are available using fragment-based chemical similarity searc...

    Authors: Syed Asad Rahman, Matthew Bashton, Gemma L Holliday, Rainer Schrader and Janet M Thornton

    Citation: Journal of Cheminformatics 2009 1:12

    Content type: Software

    Published on:

  10. The need to have a quantitative estimate of the uncertainty of prediction for QSAR models is steadily increasing, in part because such predictions are being widely distributed as tabulated values disconnected ...

    Authors: Robert D Clark

    Citation: Journal of Cheminformatics 2009 1:11

    Content type: Research article

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  11. Since 2004 public cheminformatic databases and their collective functionality for exploring relationships between compounds, protein sequences, literature and assay data have advanced dramatically. In parallel...

    Authors: Christopher Southan, Péter Várkonyi and Sorel Muresan

    Citation: Journal of Cheminformatics 2009 1:10

    Content type: Research article

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  12. We report on the implementation of the Spectral Game, a web-based game where players try to match molecules to various forms of interactive spectra including 1D/2D NMR, Mass Spectrometry and Infrared spectra. ...

    Authors: Jean-Claude Bradley, Robert J Lancashire, Andrew SID Lang and Antony J Williams

    Citation: Journal of Cheminformatics 2009 1:9

    Content type: Software

    Published on:

  13. A method to estimate ease of synthesis (synthetic accessibility) of drug-like molecules is needed in many areas of the drug discovery process. The development and validation of such a method that is able to ch...

    Authors: Peter Ertl and Ansgar Schuffenhauer

    Citation: Journal of Cheminformatics 2009 1:8

    Content type: Research article

    Published on:

  14. In ligand-based screening, as well as in other chemoinformatics applications, one seeks to effectively search large repositories of molecules in order to retrieve molecules that are similar typically to a sing...

    Authors: Ramzi J Nasr, S Joshua Swamidass and Pierre F Baldi

    Citation: Journal of Cheminformatics 2009 1:7

    Content type: Research article

    Published on:

  15. The inverse-QSAR problem seeks to find a new molecular descriptor from which one can recover the structure of a molecule that possess a desired activity or property. Surprisingly, there are very few papers pro...

    Authors: William WL Wong and Forbes J Burkowski

    Citation: Journal of Cheminformatics 2009 1:4

    Content type: Research article

    Published on:

  16. This article coincides with the 40 year anniversary of the first published works devoted to the creation of algorithms for computer-aided structure elucidation (CASE). The general principles on which CASE meth...

    Authors: Mikhail Elyashberg, Kirill Blinov, Sergey Molodtsov, Yegor Smurnyy, Antony J Williams and Tatiana Churanova

    Citation: Journal of Cheminformatics 2009 1:3

    Content type: Research article

    Published on:

  17. The advent of the Internet has been the impetus for the Open Access movement, a movement focused on expanding access to information principally by reducing the costs of journals. I argue here that the Open Acc...

    Authors: Steven M Bachrach

    Citation: Journal of Cheminformatics 2009 1:2

    Content type: Commentary

    Published on:

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