2P2Idb: a structural database dedicated to orthosteric modulation of protein-protein interactions

• Published in: Nucleic acids research 2013-01, Vol.41 (Database issue), p.D824-D827
• Main Authors: Basse, Marie Jeanne, Betzi, Stéphane, Bourgeas, Raphaël, Bouzidi, Sofia, Chetrit, Bernard, Hamon, Véronique, Morelli, Xavier, Roche, Philippe
• Format: Article
• Language: English
• Subjects: Databases, Protein; Internet; Multiprotein Complexes - chemistry; Multiprotein Complexes - drug effects; Protein Interaction Mapping; Protein Structure, Secondary; Software; User-Computer Interface
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gks1002

Protein-protein interactions are considered as one of the next generation of therapeutic targets. Specific tools thus need to be developed to tackle this challenging chemical space. In an effort to derive some common principles from recent successes, we have built 2P2Idb (freely accessible at http://2p2idb.cnrs-mrs.fr), a hand-curated structural database dedicated to protein-protein interactions with known orthosteric modulators. It includes all interactions for which both the protein-protein and protein-ligand complexes have been structurally characterized. A web server provides links to related sites of interest, binding affinity data, pre-calculated structural information about protein-protein interfaces and 3D interactive views through java applets. Comparison of interfaces in 2P2Idb to those of representative datasets of heterodimeric complexes has led to the identification of geometrical parameters and residue properties to assess the druggability of protein-protein complexes. A tool is proposed to calculate a series of biophysical and geometrical parameters that characterize protein-protein interfaces. A large range of descriptors are computed including, buried accessible surface area, gap volume, non-bonded contacts, hydrogen-bonds, atom and residue composition, number of segments and secondary structure contribution. All together the 2P2I database represents a structural source of information for scientists from academic institutions or pharmaceutical industries.