Predict protein interaction surface with the ARDOCK server¶

Scientific Purposes¶

ArDock is a structural bioinformatics web server for the prediction and the visualization of potential interaction regions at protein surfaces. Many biological function rely on the formation of protein-protein complexes. The identification protein interaction region is therefore of critical interest for our understanding of biology. The service is accessible through a web interface, both for submission and the reporting of results.

How it works ?¶

ArDock ranks the surface residues of a protein according to their tendency to form interfaces in a set of predefined docking experiments between the query protein and a set of arbitrary protein probes. The ArDock methodology is derived from large scale cross-docking studies where it was observed that randomly chosen proteins tend to dock in a non-random way at protein surfaces. This method is implemented on a computational cluster, where docking calculations run in parallel and results are aggregated and returned to the web client.

Inputs¶

• A protein structure in PDB format

• Tokens obtained in previous analysis can be given to the server to restore their results

Outputs¶

• Interactive and 3D vizualisation of the results on the protein structure

• Interactive scoreboard of the protein residue scores

• Result files available for download in CSV and PDB formats

Targeted audience¶

All scientists working in biology related areas where protein study is relevant with a focus on structural biologists and biochemists.

Additional resources¶

• A tutorial was set up by the Ardock team

• Publications describing methods and implementations

• The public database of protein structures is avaible at the PDB web site