Java Protein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure

Goran Neshich 1 Walter Rocchia 2 Adauto Mancini 1 Michel Yamagishi 1 Paula Kuser 1 Renato Fileto 1 Christian Baudet 1 Ivan Pinto 1 Arnaldo Montagner 1 Juliana Palandrani 1 João Krauchenco 1 Renato Torres 1 Savio Souza 1 Roberto Togawa 3 Roberto Higa 1
1 NBI - Núcleo de Bioinformática Estrutural
2 NEST CNR-INFM and Dipartimento di Fisica
3 Laboratório de Bioinformática
Abstract : Java Protein 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 para-meters with the potential to provide new insights into the sequence–structure–function relationship. In J PD, residue selection can be performed according to multiple criteria. J PD 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 homolo-gous structures. In order to focus on the physico-chemical (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/ (Option: Java Protein Dossier)
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Nucleic Acids Research, Oxford University Press, 2004, Web Server issue, 32, pp.W595-W601. 〈10.1093/nar/gkh480〉
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Goran Neshich, Walter Rocchia, Adauto Mancini, Michel Yamagishi, Paula Kuser, et al.. Java Protein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure. Nucleic Acids Research, Oxford University Press, 2004, Web Server issue, 32, pp.W595-W601. 〈10.1093/nar/gkh480〉. 〈hal-01092990〉

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