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)

• OSX 10.6: F2DockServer, TexMol
• OSX 10.5: F2DockServer, TexMol

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