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Nucleic Acids Research 2005 33(Web Server Issue):W29-W35; doi:10.1093/nar/gki397
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© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

The Diamond STING server

Goran Neshich*, Luiz C. Borro, Roberto H. Higa, Paula R. Kuser, Michel E. B. Yamagishi, Eduardo H. Franco, Joao N. Krauchenco, Renato Fileto, André A. Ribeiro, George B. P. Bezerra, Thiago M. Velludo, Tomás S. Jimenez, Noboru Furukawa2, Hirofumi Teshima2, Koji Kitajima2, Abdulla Bava2, Akinori Sarai2, Roberto C. Togawa1 and Adauto L. Mancini

Núcleo de Bioinformática Estrutural, Embrapa/Informática Agropecuária Campinas, Brazil 1Laboratório de Bioinformática, Embrapa/Recursos Genéticos e Biotecnologia Brasilia, Brazil 2Department of Bioscience and Bioinformatics, Kyushu Institute of Technology (KIT) Iizuka, Japan

*To whom correspondence should be addressed. Tel: +55 19 3789 5774; Fax: +55 19 3289 9594; Email: neshich{at}cnptia.embrapa.br

Received March 11, 2005. Revised March 14, 2005. Accepted March 14, 2005.

Diamond STING is a new version of the STING suite of programs for a comprehensive analysis of a relationship between protein sequence, structure, function and stability. We have added a number of new functionalities by both providing more structure parameters to the STING Database and by improving/expanding the interface for enhanced data handling. The integration among the STING components has also been improved. A new key feature is the ability of the STING server to handle local files containing protein structures (either modeled or not yet deposited to the Protein Data Bank) so that they can be used by the principal STING components: JavaProtein Dossier (JPD) and STING Report. The current capabilities of the new STING version and a couple of biologically relevant applications are described here. We have provided an example where Diamond STING identifies the active site amino acids and folding essential amino acids (both previously determined by experiments) by filtering out all but those residues by selecting the numerical values/ranges for a set of corresponding parameters. This is the fundamental step toward a more interesting endeavor—the prediction of such residues. Diamond STING is freely accessible at http://sms.cbi.cnptia.embrapa.br and http://trantor.bioc.columbia.edu/SMS.


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