pyDockDNA is a new protein-DNA rigid-body docking and scoring method

The pyDockDNA web server implements a new docking method for the structural modeling of protein-DNA interactions. The input data are the coordinates of a protein (or a multi-protein assembly) and a DNA molecule (single or double chain). The algorithm is based on the pyDock docking and scoring scheme, using FTDOCK to generate the protein-DNA orientations, and a scoring function parameterized for DNA. The output will be a set of docking models represented in different formats:

- 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).


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To cite pyDockDNA, please reference:

Rodríguez-Lumbreras LA, Jiménez-García B, Giménez-Santamarina S and Fernández-Recio J (2022) pyDockDNA: A new web server for energy-based protein-DNA docking and scoring. Front. Mol. Biosci. 9:988996. DOI: 10.3389/fmolb.2022.988996