pyDockDNA is a new protein-DNA rigid-body docking and scoring method
- The 3D structure of the best 10 docking models in terms of scoring can be visualized in the output screen.
- The PDB files for the best 100 models can be directly downloaded.
- The rotation/translation vectors are provided to generate up to a total of 10,000 docking poses.
The web server has been tested on an available protein-DNA docking benchmark (van Dijk M, Bonvin AM (2008) Nucleic Acids Res. 36:e88). Using the unbound coordinates of the interacting protein and modelled DNA molecules, the success rate for the 10 best-scoring models was 23%, which increased to 38% when using a scoring function without desolvation (averaged over 10 executions with random initial rotations of the interacting molecules, and clustered afterwards to remove redundant models).