FAQ and Help


Tutorial

There is a pyDockRescoring server tutorial which you can follow here.


Input data

PyDockRescoring server uses the results from the pyDockWEB protein-protein docking server.
PyDockRescoring server only requires a finished job url. If you are not familiar with pyDockWEB server, please use the option "Load sample data".


PyDockWEB job url

This is the unique results page generated by any pyDockWEB server submitted job.
For example: http://life.bsc.es/servlet/pydock/info/d57729df8a4fb0025cacb8c8be80078c.


Email address

The email address is optional and only used to notify the user once the job has been finished.


Democratic scoring

This scoring function used as a rescoring function of the top 500 predicted solutions by pyDockWEB server is described in the reference section, but it is based on a process which integrates biophysical properties combined using the Schulze voting system [Schulze, M. Soc. Choice Welf. 36, 267–303 (2011)].


Reference

To cite pyDockRescoring server, please reference:

Moal, I.H., Barradas-Bautista, D., Jiménez-García, B., Torchala, M., van der Veide, A, Vreven, T., Weng, Z., Bates, P.A., Fernández-Recio, J. (2017) IRaPPA: Information retrieval based integration of biophysical models for protein assembly selection. Bioinformatics 33, 1806-1813.


Result files

Once the computation has ended, the server prepares a gzip compressed tar archive containing several result files organized by folders in the following way:

Note: "[xxx]" is a numeric identifier.

results

This folder contains the files generated by pyDockRescoring server:

  • project_[xxx].[ene|eneRST].scoring_function: This file is the reranked version of the top 500 structures predicted by the pyDockWEB server. Please, check pyDockWEB documentation.
  • project_[xxx].pdb: Top100 PDB structures predicted. The numeric identifier corresponds with the table displayed in the result files (Conf column).