Nucleic Acids Research Advance Access originally published online on May 20, 2008
Nucleic Acids Research 2008 36(Web Server issue):W47-W54; doi:10.1093/nar/gkn285
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W47-W54
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Superimposé: a 3D structural superposition server
1Charité-Universitätsmedizin Berlin, Structural Bioinformatics Group, Arnimallee 22, 14195 Berlin, 2Graduate School: Genomics and Systems Biology of Molecular Networks, Monbijoustr. 2, 10117 Berlin, 3Institut für Molekularbiologie und Bioinformatik, Charité-Universitätsmedizin Berlin, Arnimallee 22, 14195 Berlin, Germany, 4Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla CA 92093-0743, USA, 5University of Vigo, Computer Science Department, 32004 Ourense, Spain, 6Georg-August-Universität Göttingen, Medical University, Robert-Koch-Str. 42, 37075 Göttingen, 7Charité, Computational Systems Biochemistry Group, Monbijoustr. 2, 10117 Berlin, 8Freie Universität Berlin, Institut für Chemie und Biochemie, Takustr. 6, 14195 Berlin, 9Universität Bayreuth, Physikalisches Institut, 95440 Bayreuth and 10Humboldt-Universität zu Berlin, Algorithms and Complexity, Unter den Linden 6, 10099 Berlin, Germany
*To whom correspondence should be addressed. Tel: +49 30 8445 1649; Fax: +49 30 8445 1551; Email: robert.preissner{at}charite.de
Received February 22, 2008. Revised April 10, 2008. Accepted April 26, 2008.
The Superimposé webserver performs structural similarity searches with a preference towards 3D structure-based methods. Similarities can be detected between small molecules (e.g. drugs), parts of large structures (e.g. binding sites of proteins) and entire proteins. For this purpose, a number of algorithms were implemented and various databases are provided. Superimposé assists the user regarding the selection of a suitable combination of algorithm and database. After the computation on our server infrastructure, a visual assessment of the results is provided. The structure-based in silico screening for similar drug-like compounds enables the detection of scaffold-hoppers with putatively similar effects. The possibility to find similar binding sites can be of special interest in the functional analysis of proteins. The search for structurally similar proteins allows the detection of similar folds with different backbone topology. The Superimposé server is available at: http://bioinformatics.charite.de/superimpose.
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