PPIDD: an extraction and visualisation method of biological protein-protein interfaces.
Today, the information for generating reliable protein-protein complex datasets is not directly accessible from PDB structures. Moreover, in X-ray protein structures, different types of contacts can be observed between proteins: contacts in homodimers or inside heterocomplexes considered to be specific, and contacts induced by crystallogenesis processes, considered to be non-specific. However, none of the databases giving access to protein-protein complexes allows the crystallographic interfaces to be distinguished from the biological interfaces. For this reason we developed PPIDD (Protein-Protein Interface Description Database), an innovative tool, which allows the extraction and visualisation of biological protein-protein interfaces from an annotated subset of crystallographic structures of proteins. This tool is focused on the description of protein-protein interfaces corresponding to well-identified classes of protein assemblies. It permits the representation of any of these protein-protein assemblies (duplex) and their interfaces as well as the export of the corresponding molecular structures under a flexible format, which is an extension of the PDBML. Moreover, PPIDD facilitates the construction of subsets of interfaces presenting user-specified common characteristics, to enhance the understanding of the determinants of specific protein-protein interactions.
Benoit
Vincent
V
Centre de Génétique Moléculaire, UPR2167, Gif/Orsay DNA MicroArray Platform, F-91198 Gif-sur-Yvette, France.
Mucchielli-Giorgi
Marie-Hélène
MH
Dumont
Benoît
B
Durosay
Patrice
P
Reymond
Nancie
N
Delacroix
Hervé
H
D018360:Crystallography, X-Ray; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D008958:Models, Molecular; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein; D014584:User-Computer Interface
D011506:Proteins