The Sys2Diag unit has developed various computer tools that it makes available for non-commercial use.
By clicking here > access to PEPOP
Prediction of antigenic and / or immunogenic peptides (PEPOP Moreau et al., 2008)): representative peptides of the protein of interest are predicted from its 3D structure. These peptides can be used to localize an epitope, obtain Acs targeting a particular area of the protein, obtain antibody pairs targeting two distinct areas of a molecule to develop a sandwich immunoassay, etc.
By clicking here > access to DUP
DUP is a database that references all of the normal urinary proteins described in the proteomic analysis articles. Currently DUP contains more than 1800 non-redundant proteins observed in at least 1 of the 12 publications studied. DUP contains general information such as the name of the protein or its molecular weight, information on the description of the protein as well as its sequence; the link with the quoted articles is also available interactively. The list of normal urinary proteins can be viewed using an easy-to-use web interface. Several tools make it easy to query the database: two tools make it possible to search for a protein from its SwissProt / IPI accession number, keyword or by sequence similarity. The set of proteins can be represented in the form of a virtual 2D gel using an interactive graphical tool. Today, the DUP database is the only database allowing a global vision of the urinary proteome and could serve as a reference for the identification of urinary biomarkers in various renal diseases.
By clicking here > Access to Sili2DGel page
Sili2DGel is an algorithm for automatic spot alignment that uses data from recursive gel matching and returns meaningful Spot Alignment Positions (SAP) for a given set of gels. It is based on graph theory in which the data are represented by a graph and SAP by specific subgraphs. The results are returned under various forms (clickable synthetic gel, text file, etc.). To run Sili2DGel, you have to install JRE. Sili2DGel needs a recursive alignment result file (tabular file of this form) and spot coordinate file (tabular file of this form). Gamma is comprised between 0 and 1; strengh is comprised between 0 and 2.
By clicking here > Access to BioNetCAD page
BioNetCAD is a CellDesigner (http://www.celldesigner.org/) plug-in, is a computer assisted design tool for synthetic biology. BioNetCAD allows designing abstract networks that can be implemented thanks to CompuBioTicDB, a database of parts for synthetic biology.