GWIDD: A genome-wide protein-protein docking database

Protein-protein interactions play essential roles in almost all aspects of cell´s functioning, from cell respiration, to cell communication, to cell cycle. Knowing the structural details of a protein-protein interaction helps us understand the mechanism of such interaction, and thus the function of participating proteins. Although the gold standard of protein structures is X-ray crystallography, crystal structures of protein complexes are more difficult to get than individual proteins. Furthermore, many protein interactions are transient, which makes studying them by crystallography and NMR even more problematic. Therefore most of the protein complex structures need to be modeled computationally. At present, docking is the most advanced method of modeling protein complex structures. We developed a comprehensive database containing genome wide protein-protein interactions from various sources and computationally modeled structures of these protein complexes using our docking methodology GRAMM-X. All data and servers of the database are freely available through a web interface. With further advancement of protein-protein interaction prediction methods and docking methodology, this database will be a valuable resource for studying protein-protein interactions.