How it works
CB-Dock was designed to perform blind docking at predicted sites, instead of the entire surface of protein. Therefore, the first step is to detect putative binding sites (Cavity detection). Since the ligand binding sites are usually some larger cavities, we select several top cavities according to cavity size for further analysis (Cavity sorting). And then, we need to set the docking center, adjust the docking box size. These parameters are required for molecular docking with AutoDock Vina (Center and Size). After the docking process finished, a series of bound poses are reranked according to the docking score (Dock and Rerank). The first conformation is considered as the best binding pose and the corresponding site is the optimal binding site for the qurey ligand. The figure below shows the workflow of CB-Dock.
After submitting the required documents, the above process is done automatically by perl script. The "Curvature" and "Clusters" program used in the process are both prepared and compiled in C++. "AutoDock Vina" is the latest 1.1.2 version. Users can download the above scripts and programs here.
Since the parameters required for docking with AutoDock Vina are automatically calculated by CB-Dock, the user simply submits a target protein as well as a query ligand and enters the number of cavities for docking (the default value is 5) under Dock.
Please note the following issues when submitting jobs:
- Target protein:
- The target protein is uploaded in PDB format. We will help you to remove all of the heteroatoms (include small molecules, ions and crystal water) in the protein before docking. [Example file]
Suggestion: If the protein is a biological assembly, you can split it into chains for docking (Split Chains).
- Query ligand:
- The ligand can be uploaded in MOL2, MOL, SDF, or PDB format. if the uploaded format is MOL, SDF, or PDB, we will transfer it to MOL2 file by Open Babel. [Example file]
Suggestion: The ligand file size should be less than 15KB. Because as the number of atoms and rotatable bonds increase, the accuracy and efficiency of AutoDock Vina will be reduced.
- Number of cavities for docking:
- The default value is 5, user can click the "More parameters" to customize this value. Program will porform docking in each of the selected cavity and the first conformation in each cavity will be chosen to rerank.
Suggestion: The maximum should be less than 20. Because as the number increase, the cost and false positive rate will be increased.
Guests can submit one blind docking job at a time. The results will be displayed under Results when we processed your input. If you close the website or your browser the session on our page may end and we won't be able to display your results. If you register as a user, you can run up to 3 blind docking jobs at the same time. Further, you may close our page and check your results whenever you like to. We store up to 6 runs on our server. If you generate more the 6 runs in one session we will delete runs starting from the oldest run on login.
After we processed your data you can download the results under Results and delete all files from our server independent if you are a registered user or guest. We automatically delete data from guest users after one day.
We tested CB-Dock using the latest three versions of IE, Edge, Firefox, Chrome and Safari. If you are using one of the before mentioned browsers and you have problems displaying the “Results” page, we recommend you to update your browser to the latest version. Some browsers may not support WebGL or don’t support all WebGL features needed by NGL viewer like Opera. Please try another browser in the case you get a warning that WebGL is not supported or the example provided by us on the “Results” page is not visible.
The latest version was modified in July 10, 2018.
Install Open Babel, if the format of query ligand is not MOL2.
sudo apt-get install openbabelInstall AutoDock Tools for Linux. AutoDock Vina uses the PDBQT molecular structure file format as its input and output. PDBQT files can be generated and viewed using MGLTools.
Enter the command through terminal:
perl AutoBlindDock.pl [Receptor] [Ligand] [CavityNum] [UserDir]
Data and results of each user are not accessible to other users, but we cannot guarantee full privacy.
Data retention policy
Data and results will be stored on the server only for a limited amount of time. The content of the server will be periodically deleted.
Currently we delete data of guest accounts after one day and data of registered accounts if more than 6 runs are stored on our sever (starting from the oldest run). Both kind of user may directly delete the data stored from our server, using the delete button under Results. We reserve the right to adjust the data retention policy depending on the workload of our server.