Instruct Image Processing Center

Information Integration Projects

Welcome to the Information Integration Projects a joint initiative of the National Institute of Bioinformatics (INB) and the INSTRUCT Center for Image Processing in Microscopy. The main goal is the development of tools and methods for helping users in the construction of hybrids models and understanding the function of macromolecular complexes.

PeppeR

PeppeR is the Java-based, graphical DAS client, intended for visualization of hybrid models (3D-EM volume maps plus atomic resolution structures from fitting experiments) together with their annotations. PeppeR implements DASx3DEM, an extension of the DAS protocol that allows sharing annotations about hybrid models. This annotation system has been built on the basis of the EMDB, which stores Three-dimensional Electron Microscopy (3D-EM) volumes, PDB, which houses atomic coordinates, and UniProt (for protein sequences) databases. In this way, annotations for sequences, atomic coordinates, and 3D-EM volumes are collected and displayed through a single graphical visualization client. Thus, users have an integrated view of all the annotations together with the whole macromolecule (3D-EM map coming from EMDB), the atomic resolution structures fitted into it (coordinates coming from PDB) and the sequences corresponding to each of the structures (from UniProt).


Data Integration for Molecular Reconstruction

DIMERO is a web based envirnoment designed to integrate bioinformatics-like information for the analysis and modelling of quaternary structures. The first version of the application introduces the use of molecular interaction data to evaluate contacts between proteins of a complex. Protein contacts are scored in terms of their domain-domain interactions (DDI) defined according the Pfam classification and a distance threshold bewteen C-α atoms. DDI scores are derived from extense protein-protein interaction (PPI) datasets computing the obseved frequency by means of statistical measures. STRING database has been selected as source of PPI knowledge, this database not only includes information from experimental sources but also predictions from genetic and phylogentic distances and mining the scientific literature. The platform will be available as a Cimera plugin and as a web server application.