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
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
- 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.
.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
can submit docking jobs with these intermediate files. This helps speed
things up when docking with the same molecules while playing with
- View Results
- Once a job is completed, the results can be stored and displayed
- First an UI displays the summary/highlights of the results
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.
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.
- Here is the user guide for F2DockClient. More detailed is available in this longer tutorial. For installation notes, refer to TexMol's user guide.