[ description ]

RbDg is a program that generates residue-based diagrams of proteins. RbDg can be thought of as a batch version of RbDe (the residue-based diagram editor), with added features. Added features include the ability to generate diagrams for different protein families. The layout of the different secondary structure elements of a protein is configured through an input file. This makes RbDg very useful to produce diagrams of proteins for databases such as GPCRDB or NuclearDB.

Usage of RbDg is summarized on the following Figure:

Generating diagrams of proteins with RbDg requires three steps. Step 1 assembles the definition of the layout of the subunits with the sequence and residue properties to display on the diagram. Step 2 processes input files to produce diagram images in the graphics formats supported by RbDg and creates an XML output. Step 3 converts the XML output of RbDg to an HTML file that includes the diagram images. Each step is further documented below.

[ about the method ]

[ documentation ]

RbDg can be started with the command $CROVER/bin/rbdg -i input.xml to process one input file, or can process a list of input files with the command $CROVER/bin/rbdg -list list-of-inputs. The latter option provides important speedups when multiple diagrams are being generated.

Sample input for a nuclear receptor

Sample input for a G Protein-Coupled receptor

The input file is an XML file that adheres to specific conventions (described in an XML schema). The schema for the input file is described here:

XML Schema documentation for the input format

Secondary structure subunits for RbDg input

XML schema for RbDg input

When RbDg processes input files, it produces output files according to the instructions given in the input. RbDg can create images in GIF or SVG format. SVG is a vectorial format, and thus can produce high-quality illustrations when printed. (SVG can also be imported in Illustrator 10+ to edit the diagrams, add annotations, etc.). Example of images produced with RbDg are shown below (SVG format may require a plugin):

Nuclear receptor GIF diagram

GPCR SVG diagram

RbDg also produces an XML output file, that documents the file produced by the command and can be transformed to HTML. This is intended to allow database curators to customize the look and feel of the page that presents the diagrams to match aesthetic conventions of the database. Schema, documentation and a sample output file are provided here:

XML Schema documentation for the output format

XML schema for RbDg output

Sample RbDg output

RbDg output can be transformed with XSL templates to produce HTML files (other formats are possible also). The following shows a sample template and the HTML output that it produces:

Sample XSL transformation

HTML produced after transformation

[ availability ]

RbDg is used to create diagrams for several biological databases (for instance GPCRDB, PDZBase, Arcadia, GPCR Natural Variants database and TRansporter Annotation Center (TRAC)).

RbDg is distributed under a license. The license is free of charge for academic institutions to use in support of education and academic research, provided that the diagrams generated with RbDg are made available at no charge to the research community. For more information about RbDg, please contact Fabien Campagne.