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  1. Authors: Jens Krüger, Georg Birkenheuer, Dirk Blunk, Sebastian Breuers, André Brinkmann, Gregor Fels, Sandra Gesing, Richard Grunzke, Oliver Kohlbacher, Nico Kruber, Ulrich Lang, Lars Packschies, Ralph Müller-Pfefferkorn, Sonja Herres-Pawlis, Patrick Schäfer, Hans-Günther Schmalz…

    Citation: Journal of Cheminformatics 2011 3(Suppl 1):O17

    Content type: Oral presentation

    Published on:

    This article is part of a Supplement: Volume 3 Supplement 1

  2. The shape diversity of 16.4 million biologically relevant molecules from the PubChem Compound database and their 1.46 billion diverse conformers was explored as a function of molecular volume.

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

    Citation: Journal of Cheminformatics 2011 3:9

    Content type: Research article

    Published on:

  3. Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-ene...

    Authors: Noel M O'Boyle, Tim Vandermeersch, Christopher J Flynn, Anita R Maguire and Geoffrey R Hutchison

    Citation: Journal of Cheminformatics 2011 3:8

    Content type: Software

    Published on:

  4. Standard approaches to address the performance of predictive models that used common statistical measurements for the entire data set provide an overview of the average performance of the models across the ent...

    Authors: Norman C LeDonne Jr, Kevin Rissolo, James Bulgarelli and Leonard Tini

    Citation: Journal of Cheminformatics 2011 3:7

    Content type: Research article

    Published on:

  5. In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure...

    Authors: Andrei A Gakh, Michael N Burnett, Sergei V Trepalin and Alexander V Yarkov

    Citation: Journal of Cheminformatics 2011 3:5

    Content type: Methodology

    Published on:

  6. PubChem, an open archive for the biological activities of small molecules, provides search and analysis tools to assist users in locating desired information. Many of these tools focus on the notion of chemica...

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

    Citation: Journal of Cheminformatics 2011 3:4

    Content type: Research article

    Published on:

  7. The decomposition of a chemical graph is a convenient approach to encode information of the corresponding organic compound. While several commercial toolkits exist to encode molecules as so-called fingerprints...

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

    Citation: Journal of Cheminformatics 2011 3:3

    Content type: Research article

    Published on:

  8. The reliable and robust estimation of ligand binding affinity continues to be a challenge in drug design. Many current methods rely on molecular mechanics (MM) calculations which do not fully explain complex m...

    Authors: Michael P Mazanetz, Osamu Ichihara, Richard J Law and Mark Whittaker

    Citation: Journal of Cheminformatics 2011 3:2

    Content type: Research article

    Published on:

  9. We collected data from over 80 different cytotoxicity assays from Pfizer in-house work as well as from public sources and investigated the feasibility of using these datasets, which come from a variety of assa...

    Authors: Sarah R Langdon, Joanna Mulgrew, Gaia V Paolini and Willem P van Hoorn

    Citation: Journal of Cheminformatics 2010 2:11

    Content type: Research article

    Published on:

  10. Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clu...

    Authors: Rui MV Abreu, Hugo JC Froufe, Maria João RP Queiroz and Isabel CFR Ferreira

    Citation: Journal of Cheminformatics 2010 2:10

    Content type: Software

    Published on:

  11. A collection of primitive operations for molecular diagram sketching has been developed. These primitives compose a concise set of operations which can be used to construct publication-quality 2 D coordinates ...

    Authors: Alex M Clark

    Citation: Journal of Cheminformatics 2010 2:8

    Content type: Research article

    Published on:

  12. OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical...

    Authors: Barry Hardy, Nicki Douglas, Christoph Helma, Micha Rautenberg, Nina Jeliazkova, Vedrin Jeliazkov, Ivelina Nikolova, Romualdo Benigni, Olga Tcheremenskaia, Stefan Kramer, Tobias Girschick, Fabian Buchwald, Joerg Wicker, Andreas Karwath, Martin Gütlein, Andreas Maunz…

    Citation: Journal of Cheminformatics 2010 2:7

    Content type: Research article

    Published on:

  13. 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

    Content type: Software

    Published on:

  14. QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, bu...

    Authors: Ola Spjuth, Egon L Willighagen, Rajarshi Guha, Martin Eklund and Jarl ES Wikberg

    Citation: Journal of Cheminformatics 2010 2:5

    Content type: Methodology

    Published on:

  15. Citation: Journal of Cheminformatics 2010 2(Suppl 1):O20

    Content type: Oral presentation

    Published on:

    This article is part of a Supplement: Volume 2 Supplement 1

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