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      The Blue Obelisk—Interoperability in Chemical Informatics

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          Abstract

          The Blue Obelisk Movement ( http://www.blueobelisk.org/) is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, open data, and open standards. We outline recent examples of cooperation in the Blue Obelisk group:  a shared dictionary of algorithms and implementations in chemoinformatics algorithms drawing from our various software projects; a shared repository of chemoinformatics data including elemental properties, atomic radii, isotopes, atom typing rules, and so forth; and Web services for the platform-independent use of chemoinformatics programs.

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          Most cited references13

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          A solution for the best rotation to relate two sets of vectors

          W Kabsch (1976)
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            The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo-and Bioinformatics

            The Chemistry Development Kit (CDK) is a freely available open-source Java library for Structural Chemo-and Bioinformatics. Its architecture and capabilities as well as the development as an open-source project by a team of international collaborators from academic and industrial institutions is described. The CDK provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Application scenarios as well as access information for interested users and potential contributors are given.
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              Van der Walss Radii of elements

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                Author and article information

                Journal
                J Chem Inf Model
                J Chem Inf Model
                ci
                jcisd8
                Journal of Chemical Information and Modeling
                American Chemical Society
                1549-9596
                1549-960X
                22 February 2006
                22 May 2006
                : 46
                : 3
                : 991-998
                Affiliations
                Pennsylvania State University, University Park, Pennsylvania 16804-3000, Jmol Project, U. S. A., Cornell University, Ithaca, New York 14853, Cambridge University, Cambridge CB2 1TN, Great Britain, Imperial College, London SW7 2AZ, Great Britain, Cologne University Bioinformatics Center (CUBIC), Zülpicher Str. 47, D-50674 Köln, Germany, University of Tübingen, Tübingen, Germany, and Jmol project, The Netherlands
                Author notes
                [†]

                 Pennsylvania State University.

                [‡]

                 Jmol project, http://www.jmol.org.

                [§]

                 Cornell University.

                [‖]

                 Cambridge University.

                [⊥]

                 Imperial College.

                 Corresponding author phone:  +49 (0)221 470-7426; fax:  +49 (0) 221 470-7786; e-mail:  c.steinbeck@uni-koeln.de.
                [#]

                 Cologne University Bioinformatics Center.

                [∇]

                 University of Tübingen.

                [○]

                 Jmol project, http://www.jmol.org.

                Article
                10.1021/ci050400b
                4878861
                16711717
                2ae3d5e7-a6ef-44b2-8731-3c7989aaa3e4
                Copyright © 2006 American Chemical Society

                This is an open access article published under a Creative Commons Attribution (CC-BY) License, which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.

                History
                : 12 September 2005
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                ci050400b

                Computational chemistry & Modeling
                Computational chemistry & Modeling

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