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

Abstract

JavaProtein Dossier ( J PD) 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 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 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. J PD is freely accessible (within the Gold Sting Suite) at

Identification of snake bradykinin-potentiating peptides (BPPs)-simile sequences in rat brain – Potential BPP-like precursor protein?

“…Additionally, we used STING server [47] to generate the "TGZ" file containing all STING structure descriptors. The TGZ file was used as input to Java Protein Dossier [48], in order to analyze other physical-chemical features of amino acids for a given 3D configuration. PyMol [49] was then used to generate the molecular images.…”

Predição de função de proteínas através da extração de características físico-químicas

“…Entre os módulos do Sting_DB, há o Java Protein Dossier (JPD) [14], uma ferramenta que fornece aos usuários uma vasta coleção de parâmetros físico-químicos descrevendo a estrutura da proteína, estabilidade e interações com outras macromoléculas.…”

Induction of Neutralizing Antibodies against Mutalysin-II from Lachesis muta muta Snake Venom Elicited by a Conformational B-cell Epitope Predicted by Blue Star Sting Data Base

“…In this work, BSS platform was used as a tool to predict a conformational epitope of Mut-II based on its physicochemical properties. For this, we used Java Protein Dossier (JPD) module of BSS [28] as a tool to select amino acids, which could form possible epitopes in the 3D model of the Mut-II. In the JPD, there is a SELECT feature that allows the user to filter conditions that may be used to select amino acid residues which satisfy all indicated numerical and/or descriptive ranges marked in the interactive SELECT window.…”

“…The BSS itself is not a program for predicting epitopes; it is a web based software for interactive analysis of the sequence/structure/function of proteins and their complexes with DNA and ligands, allowing the user to interactively analyze molecular structures, cross-referencing visualized information with correlated attributers stored in the BSS database [11]. BSS has a module, (the JPD) [28] that communicate a large set of the physicochemical properties of proteins at a residueby-residue level through a unique graphic interface. JPD currently connects to a total of 1540-numerical/textual descriptors for any given protein structure deposited in the PDB in a residue by residue manner ((8.89 × 10 10 records -105000 structures with 2.2 chains in average, with 250 amino acids in average per chain) [10].…”