This web service is for the structural prediction of protein-protein interactions using an improved version of
our Fast Rotational DOCKing
method*. Given the 3D coordinates of two interacting proteins (conforming PDB format) the server generates very efficiently many potential predictions of how they could interact. Once your job is completed you can interactively check protein-protein models and add experimental constraints to refine the docking. A standard-size case usually takes only a couple of minutes to complete the docking depending of the size and computational resources available. The users can choose between scoring weighting schemes optimized for three different interaction types: Enzyme/Substrate, Antibody/Antigen, and Others to slightly improve the success rates. Please keep track of your jod ID number so you can have access to your results from the Results tab. Alternatively you can also choose to be notified by email.
New version 2020 (v3.12)
|*If you would like to refer our work use:|
|Server/Improved method||E. Ramírez-Aportela, J.R. López-Blanco, and P. Chacón (2016). FRODOCK 2.0: Fast Protein-Protein docking server. Bioinformatics, 32(15), 2386-2388. (Please, use this reference)|
|Original method||J.I. Garzón, J.R. López-Blanco, C. Pons, J. Kovacs, R. Abagyan, J. Fernández-Recio, and P. Chacón (2009). FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics, 25, 2544-2551.|
Here you can find the best docking results found in Benchmark 4.0. If you click on any of the case links, an interactive Jmol showing the first acceptable solution and the bound ligand pose will appear (note that these results are from an older version, the current Frodock server is likely to yield better results).
Here you can find all the best docking results found in Benchmark 4.0.
Please keep track of your jod ID number so you can inspect your results by input this ID in the Results tab. Results will be available for at least two months.
Once a standard-sized job is running ("r" status) it usually takes less than two minutes to complete depending on its size. As soon as any of your jobs finishes it will move to the list of "Your finished jobs" for further access and a blinking button will appear to redirect you to the Results of the last finished job.
In case you detect any problem in any of your submitted jobs they can be easily deleted by clicking the corresponding red cross. A "dr" status (black) will evidence that it is being deleted from queue. Note that anyone but you can delete your jobs.
|Distance constraints examples|
|PDB*||Interaction Type||Rank Before||Rank After||Receptor residue||Ligand residue||Distance constraint|