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. 2008 Jul 1;36(Web Server issue):W47-54.
doi: 10.1093/nar/gkn285. Epub 2008 May 20.

Superimpose: a 3D structural superposition server

Raphael A Bauer  1 , Philip E Bourne, Arno Formella, Cornelius Frömmel, Christoph Gille, Andrean Goede, Aysam Guerler, Andreas Hoppe, Ernst-Walter Knapp, Thorsten Pöschel, Burghardt Wittig, Valentin Ziegler, Robert Preissner
Affiliations

Superimpose: a 3D structural superposition server

Raphael A Bauer et al. Nucleic Acids Res. .

Abstract

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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Figures

Figure 1.
Figure 1.
Suitable combinations of databases with algorithms depending on the class of the scientific problem.
Figure 2.
Figure 2.
Query compound Chlorpromazine(red) and search hit Trimipramine (green).
Figure 3.
Figure 3.
Superposition of the active site derived from protein Hydrolase (PDB-code: 1PEK/green atoms) that is successfully identified in protein Subtilisin (PDB-code: 2SIC/cpk coloured ball and sticks in the middle).
Figure 4.
Figure 4.
Results (left) and non-sequential structural alignment generated by GangstaLite (right).
See this image and copyright information in PMC

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