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PMID: 15980473 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The Diamond STING server.

Nucleic acids research ·Vol. 33 ·No. Web Server issue ·2005-07-01 ·Pages W29-35

Neshich G, Borro LC, Higa RH, Kuser PR, Yamagishi ME, Franco EH, Krauchenco JN, Fileto R, Ribeiro AA, Bezerra GB, Velludo TM, Jimenez TS, Furukawa N, Teshima H, Kitajima K, Bava A, Sarai A, Togawa RC, Mancini AL

Abstract

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: (Java)Protein Dossier ((J)PD) 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.

MeSH Terms

Acid Anhydride Hydrolases/chemistry Amino Acids/chemistry Binding Sites Databases, Protein HIV Integrase/chemistry Internet Models, Molecular Protein Conformation Proteins/chemistry,physiology Sequence Analysis, Protein Software Systems Integration

Chemicals

Amino Acids Proteins HIV Integrase Acid Anhydride Hydrolases acylphosphatase

Authors & Affiliations

19 authors, click to expand affiliations / ORCID

Neshich Goran

Núcleo de Bioinformática Estrutural, Embrapa/Informática Agropecuária Campinas, Brazil. [email protected]

Borro Luiz C

Higa Roberto H

Kuser Paula R

Yamagishi Michel E B

Franco Eduardo H

Krauchenco Joao N

Fileto Renato

Ribeiro André A

Bezerra George B P

Velludo Thiago M

Jimenez Tomás S

Furukawa Noboru

Teshima Hirofumi

Kitajima Koji

Bava Abdulla

Sarai Akinori

Togawa Roberto C

Mancini Adauto L

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Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

1362-4962

DOI

10.1093/nar/gki397

[email protected]

Published

2005-07-01

Pages

W29-35

Language

English

Region

England

NLM ID

0411011

PMCID

PMC1160158

Subset

External Links

PubMed source DOI: 10.1093/nar/gki397 PMC Full Text View journal details

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