FRODOCK Interactive protein-protein docking

This web service is intended 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 efficiently generates 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)

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*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.

or select an example

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).

Antigen/Antibody (1FSK)
Enzyme/Substrate (1JTG)
Others (1GPW)

Here you can find all the best docking results found in Benchmark 4.0.

Antigen/Antibody (25)
PDB* Rank* Total
RMSD		 Interface
RMSD		 Fnat Fnot
1AHW 3 2.46 1.08 0.66 0.22
1BVK 1 8.19 3.80 0.17 1.08
1DQJ 263 6.59 3.47 0.23 0.30
1E6J 7 8.24 4.05 0.27 0.61
1JPS 1 4.63 0.95 0.51 0.08
1MLC 4 4.72 1.11 0.77 0.21
1VFB 5 6.97 4.01 0.17 0.94
1WEJ 1 1.57 0.77 0.74 0.26
2FD6 1 10.87 3.16 0.30 0.74
2I25 37 8.12 3.19 0.19 0.33
2VIS 12 17.70 3.04 0.20 1.04
1BJ1 10 4.69 1.42 0.57 0.10
1FSK 1 1.53 0.66 0.85 0.06
1I9R 2 8.08 1.65 0.61 0.15
1IQD 2 8.20 2.36 0.40 0.35
1K4C 329 9.32 4.01 0.13 0.44
1KXQ 1 2.96 1.02 0.86 0.20
1NCA 9 2.31 0.72 0.82 0.13
1NSN 29 5.09 2.61 0.43 0.57
1QFW 5 3.14 1.21 0.79 0.13
2QFW 1 2.36 1.42 0.73 0.16
2JEL 10 7.91 4.46 0.16 0.39
1BGX - - - - -
1E4K 642 4.15 3.84 0.27 0.42
2HMI 296 45.64 3.93 0.21 0.50
Enzyme/Substrate (52)
PDB* Rank* Total
RMSD		 Interface
RMSD		 Fnat Fnot
1AVX 1 2.21 0.80 0.75 0.17
1AY7 3 3.18 1.10 0.62 0.12
1BVN 1 2.36 1.36 0.55 0.26
1CGI 9 6.58 4.09 0.12 0.36
1CLV 3 5.03 2.51 0.31 0.34
1D6R 37 8.73 4.00 0.10 0.76
1DFJ 1 4.07 1.87 0.60 0.75
1E6E 1 7.99 2.67 0.30 0.56
1EAW 15 3.92 1.35 0.74 0.39
1EWY 9 8.68 5.00 0.15 0.90
1EZU 25 8.85 2.67 0.39 0.38
1F34 4 5.14 1.90 0.52 0.29
1FLE 15 5.90 2.67 0.24 0.45
1GL1 1 8.96 4.17 0.11 0.45
1GXD 133 15.90 3.65 0.13 0.44
1HIA 2 8.82 4.18 0.14 1.22
1JTG 1 0.86 0.60 0.71 0.32
1MAH 1 2.37 0.97 0.78 0.49
1N8O 3 2.38 1.19 0.67 0.04
1OC0 817 9.05 3.89 0.15 0.76
1OPH 294 10.00 3.90 0.61 0.65
1OYV 4 4.12 1.41 0.65 0.43
BOYV 5677 8.89 13.39 0.42 0.48
1PPE 1 0.84 0.53 0.87 0.27
1R0R 2 8.74 2.44 0.58 0.71
1TMQ 18 3.99 1.99 0.57 0.66
1UDI 4 6.99 3.37 0.25 0.52
1YVB 18 11.46 2.11 0.34 0.29
2ABZ 187 9.07 2.94 0.29 0.49
2B42 19 5.49 2.10 0.80 0.84
2J0T 68 11.14 3.88 0.17 1.52
2MTA 6 12.32 3.80 0.27 0.98
2O8V 188 9.93 3.98 0.19 0.24
2OUL 1 1.99 0.86 0.85 0.29
2PCC 10 9.65 4.01 0.33 1.23
2SIC 52 7.73 1.62 0.59 0.41
2SNI 3 5.57 1.62 0.71 0.50
2UUY 17 17.83 3.92 0.14 0.47
3SGQ 49 9.16 2.44 0.45 0.59
7CEI 1 8.32 2.48 0.53 0.55
1ACB 11 11.39 3.82 0.17 0.90
1IJK 678 8.87 2.58 0.31 0.60
1JIW 209 7.85 4.06 0.17 0.56
1KKL 67 8.79 4.56 0.14 0.58
1M10 85 9.67 4.85 0.14 0.45
1NW9 20 7.40 8.85 0.10 0.88
4CPA 10 4.60 1.65 0.83 0.94
1F6M 3871 9.92 6.47 0.21 1.23
1FQ1 2376 9.32 4.22 0.21 0.15
1PXV 48 9.31 4.75 0.24 0.45
1ZLI - - - - -
2O3B 479 10.49 3.99 0.24 0.94
Others (99)
PDB* Rank* Total
RMSD		 Interface
RMSD		 Fnat Fnot
1A2K 114 9.14 3.18 0.26 0.42
1AK4 42 9.96 4.07 0.28 0.63
1AKJ 17 8.63 4.85 0.22 1.73
1AZS 3 7.02 2.03 0.56 0.39
1B6C 1 2.57 2.07 0.80 0.32
1BUH 40 4.09 2.42 0.32 0.23
1E96 1 11.14 3.54 0.23 1.10
1EFN 272 13.39 3.51 0.38 0.33
1F51 6 9.77 5.01 0.13 0.89
1FC2 248 9.91 5.00 0.19 0.28
1FCC 1194 8.65 4.16 0.23 0.51
1FFW 1 10.59 3.38 0.44 0.33
1FQJ 17 7.28 3.10 0.37 0.30
1GCQ 33 1.73 1.03 0.71 0.10
1GHQ 1594 17.00 3.96 0.52 1.44
1GLA 25 19.10 3.92 0.18 1.21
1GPW 1 2.03 1.24 0.79 0.50
1H9D 17 8.09 4.16 0.18 0.27
1HCF 8 5.36 1.89 0.39 0.59
1HE1 99 8.47 14.85 0.16 0.33
1I4D 86 17.60 3.75 0.11 0.82
1J2J 1 9.57 3.39 0.24 0.73
1JWH 20 11.52 2.28 0.32 0.38
1K74 1 2.00 0.99 0.75 0.15
1KAC 11 10.37 3.83 0.36 0.54
1KLU 1766 10.04 2.98 0.35 0.42
1KTZ 26 18.26 2.27 0.45 0.26
1KXP 1 11.56 3.98 0.30 0.26
1ML0 1 2.64 1.36 0.71 0.37
1OFU 12 14.39 2.78 0.39 0.31
1PVH 1358 14.95 3.50 0.14 0.39
1QA9 19 8.34 3.45 0.38 0.81
1RLB 5 7.92 1.97 0.69 0.52
1RV6 1 2.88 1.50 0.68 0.40
1S1Q 33 6.12 3.13 0.26 0.79
1SBB 1731 3.40 0.85 0.79 0.61
1T6B 145 8.17 2.55 0.54 0.23
1US7 41 12.45 3.99 0.21 0.71
1WDW 1 1.71 1.53 0.52 0.21
1XD3 1 8.50 3.03 0.13 0.24
1XU1 95 7.29 2.52 0.47 0.26
1Z0K 1 9.15 3.79 0.13 0.46
1Z5Y 1 7.27 2.88 0.31 0.46
1ZHH 21 9.21 3.18 0.19 0.28
1ZHI 9 3.19 0.97 0.73 0.27
2A5T 457 5.81 3.84 0.23 0.88
2A9K 52 13.81 2.96 0.18 0.27
2AJF 336 15.94 3.96 0.17 0.56
2B4J 94 9.11 4.54 0.69 0.50
2BTF 10 6.75 3.32 0.18 0.44
2FJU 249 8.92 3.68 0.31 0.84
2G77 1 7.60 2.67 0.35 0.20
2HLE 1 3.68 1.86 0.44 0.26
2HQS 362 11.82 3.71 0.32 0.49
2OOB 87 12.17 3.30 0.39 0.43
2OOR 180 12.27 3.79 0.26 0.50
2VDB 2 3.00 0.95 0.73 0.03
3BP8 17 9.69 2.86 0.31 0.94
3D5S 1 3.87 1.71 0.46 0.27
1GP2 1 12.48 2.67 0.10 0.18
1GRN 7 3.22 1.67 0.39 0.26
1HE8 591 8.29 4.47 0.18 1.34
1I2M 1 7.00 4.42 0.17 0.60
1IB1 139 9.97 4.17 0.11 0.70
1K5D 9 5.99 2.55 0.15 0.20
1LFD 7 8.67 4.92 0.38 0.43
1MQ8 66 24.94 3.99 0.30 0.93
1N2C 8 8.08 4.17 0.17 0.24
1R6Q 1 12.78 3.81 0.39 0.57
1SYX 1 3.85 2.40 0.50 0.22
1WQ1 12 10.77 3.36 0.32 0.45
1XQS 2 10.87 3.02 0.29 0.11
2AYO 1 6.11 2.91 0.25 0.33
2CFH 7 3.31 2.18 0.34 0.50
2H7V 198 18.66 3.55 0.54 0.17
2HRK 55 6.31 2.81 0.52 0.37
2J7P 3876 9.48 5.42 0.10 0.39
2NZ8 8 9.99 5.58 0.18 0.62
2OZA 5 9.33 4.53 0.25 0.73
2Z0E 6 9.81 3.58 0.19 0.37
3CPH 9 11.06 3.62 0.13 0.36
1ATN 84 9.83 4.50 0.31 0.22
1BKD 14 6.39 4.57 0.17 0.52
1DE4 1 3.47 2.71 0.46 0.32
1EER 64 9.72 4.62 0.24 0.39
1FAK - - - - -
1H1V - - - - -
1IBR - - - - -
1IRA - - - - -
1JK9 1 4.77 2.80 0.52 0.07
1JMO - - - - -
1JZD 14 6.53 3.32 0.30 0.16
1R8S - - - - -
1Y64 - - - - -
1ZM4 2 7.97 2.80 0.60 0.46
2C0L 3391 9.93 4.14 0.14 0.51
2I9B 1109 8.63 5.01 0.11 0.38
2IDO 42 9.60 4.63 0.17 0.72
2OT3 80 9.04 5.24 0.11 0.24

First, upload the input coordinates of both ligand (smallest) and receptor (biggest) proteins in strict PDB format. Be aware of missing atoms, alternative conformations, bad placed atoms, and a long etc. that can eventually jeopardize your results. Use your favorite PDB checker (e.g. Molprobity) to anticipate and fix any potential PDB error. You can optionally introduce an email address to receive a direct link to access your results later.


Alternatively, depending of the nature of your interaction you could choose between Enzyme/Substrate, Antibody/Antigen, and Others to slightly improve the success rates. Otherwise, Unknown interaction type will be assumed.


Upon pressing the "Submit Job" button your job will be queued in our system and you will be redirected to the Queue tab. A standard-sized docking usually takes less than two minutes to complete depending on the size and computational resources available.

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.

Here all jobs submited to Frodock Server are listed. Your jobs are shown in darker colors whereas those submitted by others appear in lighter colors. You can check server usage and whether any queued job is running ("r" status, green) or queued ("qw" status, orange). In case any of your jobs has been queued ("qw" status) it will run as soon as computational resources become available.

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.

Once your job is completed you can interactively check protein-protein models and add experimental constraints to refine the docking. Results can be interactively visualized in 3D with JSmol. Use mouse controls to readily explore the solutions by visualizing multiple docking poses at the same time and toggling them between different molecular representations and colors. The user can choose between three different interfaces: Java, HTML5 and WebGL. The HTML5-javascript interface is activated by default. To activate the JAVA, first you must enable it in your web browser (see details) and add frodock.chaconlab.org to the exception sites in the Java panel (see details)


At the end of the page you can find the corresponding links to download all the files generated by the server.


In case you have distance constraints available, i.e. any biochemical or biophysical data indicating the approximate distance between two residues in the complex, it can be specified to select only the compatible poses and thus improve the ranking of the best solution. Please, expand the "Distance Constraints" panel and select two residues (one in the receptor and the other in the ligand), introduce the distance threshold (in Angstroms) in the input box, and click the "Add" button. You can specify up to ten distance constraints online. Finally, upon clicking on the "Apply constraints" button, a selector for the filtered solutions will appear in the "Load Solutions" panel. You can try any of the following constraints as practice.

Distance constraints examples
PDB* Interaction Type Rank Before Rank After Receptor residue Ligand residue Distance constraint
1NCA Antigen/Antibody 9 1 ASN-102 THR-319 5.0
1N8O Enzyme/Substrate 3 1 MET-184 MET-80 5.0
1ZHI Others 9 1 SER-113 PRO-9 5.0
1GCQ Others 33 1 THR-205 PRO-2 5.0

  1. What are the common mistakes?
    Format errors are behind of FRODOCKś malfunction in 99% of the cases. Be aware of missing atoms, alternative conformations, bad placed atoms, bad names, and a long etc. that can eventually jeopardize your results. Use your favorite PDB checker (e.g. Molprobity) to anticipate and fix any potential PDB error. Ideally, the input structures should be parsed to check errors and minimized with an external program.

  2. What are the differences in the docking algorithm and/or scoring function for different Type of interaction?
    There are none algorithm differences. Depending of the protein interaction, 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. The normalized weighting factors for Wvdw, WEle, WSAS and, Wpair are 1.0, 0.3, 0.5,15.0 for enzyme substrate cases, 1.0, 0.6, 0.5, 15.0 for antigen-antibody cases and 1.0, 1.0, 0.5, 15.0 for Others cases, respectively. And the default parameters (unknown interaction selection) are 1.0, 0.5, 0.5, 15.0. It is important to mention that compared with the addition of the pairwise potential the gain obtained in terms of docking success rates was quite reduced. The biggest improvement (~5%) was found by up weighted the electrostatic term in test cases classified as “Others”.

  3. Do the users need to run many docking jobs with different random orientations?
    Note that the reported success rates (see ROC plots in benchmark tab) are calculated with 50 docking orientations per test case. Thus, contrary to other methods, the reported success rates give a more realistic estimation of the performance as it includes the docking dependence from initial positions. Nevertheless, FRODOCK is quite robust and when is able to identify the correct pose it does in all tested rotations. However, the exact rank of best prediction found varies; for example, for the cases in where FRODOCK found acceptable solution within 2000 positions (150 cases, success rate of 84%) we found on average a variation of 100 positions. This variation logically depends on the test case and the FRODOCK’s relative sensitivity. When FRODOCK identifies the correct pose in the top 100 the average rank variation is reduced to 15 positions. Despite of this variation and given the representativeness of the benchmark, we expect success rates as displayed in in the ROC curves in benchmark tab independently of the initial receptor and ligand orientation. Therefore, the users do not need to run many docking jobs with different random orientations.

  4. ¿Visualization problems?
    3D display is based on JSmol which is very stable and compatible with all browsers. However, problems may occur. For example, reported problems with the display of the hot spots are likely related with older version of JSmol installed in the browser cache. Please be sure that the JSmol correspond to 14.40_2015.12 ( JSmol menu >> About). If not, the solution will be to clear or empty the browser's cache

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