Chandrajit Bajaj

F2Dock Front End


F2DockClient is a collection of user interfaces packaged into TexMol that allows a user to interactively submit protein-protein docking jobs to a remote computing cluster, monitor the status of the jobs and retrieve and visually display/compare the results. Advanced users can also play with a number of parameters and even control how intermediate files are generated.

  • Job Submission and Management
    • A simple UI for submitting a docking job makes it as easy as browsing and selecting two .pdb files (the receptor and the ligand)
    • A master UI allows users to submit upto 10 simultaneous jobs and monitor their progress
    • Jobs, both completed and running, can be saved and reloaded. No need to wait for a job to complete. Users can submit, save and close the application immediately. The results can be retrieved by loading the job in the future
  • Advanced Options
    • Advanced users can tweak parameters governing the weights of different scoring terms
    • Select which of the pre and post filters are applied and also tweak some of their parameters
    • Working with intermediate files and their parameters.
      • Produce .f2d files. These are generated from PDB files by first generating the .pqr file and the molecular surface and finally by separating the skin and core regions
      • Produce .quad files. These files containing integration points sampled on the surface are generated from the surface file, and is used to compute several energetics terms
      • Users can submit docking jobs with these intermediate files. This helps speed things up when docking with the same molecules while playing with different parameters
  • View Results
    • Once a job is completed, the results can be stored and displayed
    • First an UI displays the summary/highlights of the results
    • Users can then select to view the results in details in the detailed results UI. It allows the user to visually select individual conformations and
      • View the breakdown of scores of different terms
      • View interface related statistics
      • Display the smooth/UofB rendering of the complex and interact with the display
      • Multiple conformations can also be selected to display overlayed rendering of them


C. Bajaj, R. Chowdhury, and V. Siddavanahalli
F2Dock: Fast Fourier Protein-Protein Docking
To Appear in the IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009. (pdf)

Download F2Dock can be run through TexMol and set to connect to a local copy of the docking server. Binaries are available for mac. TexMol binaries included below have been pre-configured to use the local docking server.

Software Usage
  • Here is the user guide for F2DockClient. More detailed is available in this longer tutorial. For installation notes, refer to TexMol's user guide.