FAQ and Help

Input data

pyDockDNA server uses two different sources of input data:

  1. User custom PBD structures. This option is identified by the label 'Upload PDB structures'. When this option is selected, the user is asked to upload two separate PDB files, receptor and ligand structures respectively.
  2. RCSB code. This option is identified by the label 'Select PDB by RCSB code'. When the user selects this option, pyDockDNA polls the RCSB Protein Data Bank and download the PDB structure automatically (only if exists).

PDB structure files

In order to avoid invalid results for a given PDB structure, be encourage to follow the PDB file format. Note that incomplete backbone atoms may incur in inaccurate results and/or software failure.

pyDockDNA server makes use of the SCWRL software for rebuilding missing side-chains (if possible). We would like to thank the Dunbrack lab for granting us permission to use their software.


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

Distance restraints

pyDockRST software package uses the percentage of satisfied distance restraints, together with the electrostatics and desolvation binding energy, to identify correct docking orientations.
This methodology dramatically improves the docking results when compared to the use of energy criteria alone, and is able to find the correct orientation within the top 20 docking solutions in 80% of the cases. (Chelliah V. et al, J Mol Biol. 2006;357:1669-1682)

Result files

Once the computation has ended, pyDockWeb prepares a gzip compressed tar archive containing the following files ("[xxx]" is a numeric identifier):

  • project[xxx].ftdock: FTDock application output.
  • project[xxx].rot: rotation angles for each of the poses generated by FTDock.
  • project[xxx]_rec.pdb: Receptor PDB file parsed pyDockDNA.
  • project[xxx]_lig.pdb: Ligand PDB file parsed pyDockDNA.
  • project[xxx]_setup.log: A log file of the pyDock setup process (PDB files parsing).
  • project[xxx]_[scoring].ene: a table with a list of generated conformations scored and ranked by the energy scoring selected.
  • project[xxx]_*.pdb: One of the top 100 conformations in PDB file format. They correspond with the first 100 rows in project[xxx]_[scoring].ene file.

If any distance restraint has been chosen:
  • project[xxx].rst: contains a table with the top 10000 conformations scored using the restraints applied.
  • project[xxx]_[scoring].eneRST: a table with a list of generated conformations scored and ranked by the energy scoring selected and one extra column with the restraint scoring.

Protein-DNA case studies

A non-redundant additional set of protein-DNA docking cases (not included in previously available protein-DNA docking benchmark; van Dijk M, Bonvin AM (2008) Nucleic Acids Res. 36:e88) can be dowloaded here.