Das 2015

GWIDD: GENOME-WIDE DOCKING DATABASE

Madhurima Das, Petras Kundrotas and Ilya Vakser

Center for Computational Biology, The University of Kansas, Lawrence, Kansas, USA

Structural characterization of protein-protein interactions (PPI) is essential for understanding molecular mechanisms in living systems. Genome-Wide Docking Database (GWIDD) contains structurally characterized experimental and modeled protein-protein complexes, representing diverse organisms, from viruses to human. Docking algorithms are employed to generate 3D structures of PPI imported from publicly available databases. The current version of GWIDD contains 11,073 experimentally determined and 41,237 modeled PPI structures from 771 organisms. The user-friendly interface offers flexible organism-specific search with advanced functions that give more control to the user, allowing for a refined search for either one or both proteins. Users can visualize the 3D structure of a specific PPI and download the coordinates in PDB format. Evaluation of the model quality is provided for each model structure. The regularly updated GWIDD is available at http://gwidd.compbio.ku.edu.