Java Protein Dossier (JPD) is the new concept, database and visualization tool providing one of the most abundant collection of the physical chemical parameters describing the protein structure, stability, function and interaction with the other macromolecules. By collecting as many descriptors/parameters as possible within a single database (Protein Dossier), 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 reveal a new insight into the relationship sequence-structure-function. In JPD, the user may perform a complex analysis and sub setting of amino acids belonging to the molecular sequence and structure described in a PDB file, by means of a very sophisticated “JPD Select” tool. JPD may simultaneously display and analyze all the physical chemical parameters of previously superimposed structures, allowing for the direct parameter comparison at corresponding amino acid positions among homologous structures.
JPD is completely integrated with our STING Millennium (24) molecular sequence/structure viewer. All the parameters presented in JPD can be mapped on the 3D structure by means of appropriate atom coloring.
JPD has two working modes permitting its use with: A) a single PDB structure (see Figure 1) and, B), a structural alignment of two protein chains (previously aligned with the CE (15) software).
JPD displays a selection of structure parameters based on a choice of one among the three possible default views: a “Molecular Biology view”, a “Crystalograhy view” and a “view all”. An image generated by JPD is actually a user’s interface: an interactive window for accessing and graphically representing stored data. This window can be split to accommodate for the display of the parameters belonging to two protein chains. In addition, there is a menu and a speed bar with icons for the most used tasks in this window. All these components of the main JPD window are described in details in JPD HELP.
Access the JPD reference: Java Protein Dossier: a Web based program with a novel interface designed to maximize the interactivity for data visualization and comprehensive analysis of protein structure and sequence