JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure
Núcleo de Bioinformática Estrutural, Embrapa/Informática Agropecuária, Campinas, Brazil, 1 Laboratório de Bioinformática, Embrapa/Recursos Genéticos e Biotecnologia Brasilia, Brazil and 2 NEST-INFM, Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
* To whom correspondence should be addressed at EMBRAPA/CNPTIA, Structural Bioinformatics, Av. Andre Tosselo 209-Barão Geraldo, Campus UNICAMP, Campinas, SP 13083-886, Brazil. Tel: +55 19 3789 5774; Fax: +55 19 3289 9594; Email: neshich{at}cnptia.embrapa.br
Received February 13, 2004; Revised April 15, 2004; Accepted May 4, 2004
JavaProtein Dossier (JPD) is a new concept, database and visualization tool providing one of the largest collections of the physicochemical parameters describing proteins' structure, stability, function and interaction with other macromolecules. By collecting as many descriptors/parameters as possible within a single database, we can achieve a better use of the available data and information. Furthermore, data grouping allows us to generate different parameters with the potential to provide new insights into the sequence–structure–function relationship. In JPD, residue selection can be performed according to multiple criteria. JPD can simultaneously display and analyze all the physicochemical parameters of any pair of structures, using precalculated structural alignments, allowing direct parameter comparison at corresponding amino acid positions among homologous structures. In order to focus on the physicochemical (and consequently pharmacological) profile of proteins, visualization tools (showing the structure and structural parameters) also had to be optimized. Our response to this challenge was the use of Java technology with its exceptional level of interactivity. JPD is freely accessible (within the Gold Sting Suite) at http://sms.cbi.cnptia.embrapa.br, http://mirrors.rcsb.org/SMS, http://trantor.bioc.columbia.edu/SMS and http://www.es.embnet.org/SMS/ (Option: JavaProtein Dossier).
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  G. Neshich, L. C. Borro, R. H. Higa, P. R. Kuser, M. E. B. Yamagishi, E. H. Franco, J. N. Krauchenco, R. Fileto, A. A. Ribeiro, G. B. P. Bezerra, et al. The Diamond STING server Nucleic Acids Res., July 1, 2005; 33(suppl_2): W29 - W35. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Neshich, A. L. Mancini, M. E. B. Yamagishi, P. R. Kuser, R. Fileto, I. P. Pinto, J. F. Palandrani, J. N. Krauchenco, C. Baudet, A. J. Montagner, et al. STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database Nucleic Acids Res., January 1, 2005; 33(suppl_1): D269 - D274. [Abstract] [Full Text] [PDF]
|
|