IGB Molecular Interaction (MI) Bundle


  • Map genomic regions to variant splicing sequences from Uniprot.
  • Build molecular networks based on the interactions available in any database that has implemented the PSICQUIC standard web service and is available through the PSICQUIC registry.
  • Export the network in tab-delimited or xgmml files (that can be imported and analyzed in Cytoscape)
  • Filter interactions based on their type or the cumulative experimental evidence.
  • Map the genomic regions to molecular interactions structures from PDB (protein-protein, protein-nucleic acid, protein-ligand interactions) or Interactome3D (protein-protein interaction structures and models).
  • Visualize contact residues in Jmol.
  • Integration with all features and plugins from the Integrated Genome Browser.


Mapping genomic regions to proteins and structures.

The mapping is done in several steps:
  • Map gene name/refseq ID to Uniprot, using the Uniprot web service.
  • Align the transcript sequence (the sequence of each exon is extracted from the QuickLoad server, the transcript is assembled and translated) to the uniprot sequence. The alignment is done on the sequence of the splice variant rather than the one of the canonical form..
  • Align the sequence from Uniprot to the sequence of the structure, as extracted from the PDB file.

Identification of contact residues.

We calculate the available surface area (ASA) of the residues of interest in the presence and absence of the other chains. A residue is consider in contact if its ASA is reduced by at least 1 A2 in the presence of another chain. The ASA is calculated with the BioJava API (http://biojava.org/).

Molecular interactions

We query the PSICQUIC registry for the list of available PSICQUIC servers. A first query is done on each server to identify those that rely on Uniprot references. Each new server available through this registry will be automatically available from the plugin. (we plan to add the option to add manually other registries or server to the plugin). The networks are displayed by the Jung library (http://jung.sourceforge.net/).


The structures are obtained from PDB and Interactome3D, and displayed with Jmol (http://jmol.sourceforge.net/).

Evidence score

A simple score has been implemented in order to highlight the interactions with the stronger
  • * all interactions imported from a database (excluding the structure database).
  • ** interactions detected by at least two methods OR supported by at least two bibliographic references.
  • *** interactions detected by at least two methods AND supported by at least two bibliographic references.


  • PSICQUIC: Aranda,B. et al. (2011) PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods, 8, 528–529.
  • Jmol The Jmol Team (2007) Jmol: an open-source Java viewer for chemical structures in 3D.
  • Uniprot: Magrane,M. and Consortium,U. (2011) UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford)., 2011, bar009.
  • Interactome3D: Mosca,R. et al. (2013) Interactome3D: adding structural details to protein networks. Nat. Methods, 10, 47–53.
  • BioJava: Prlic,A. et al. (2012) BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics, 28, 2693–2695.
  • PDB: Velankar,S. et al. (2011) PDBe: Protein Data Bank in Europe. Nucleic Acids Res., 39, D402–D410.
  • JUNG: http://jung.sourceforge.net