Details_Automated Docking

Disclaimer: This help page applies to the webtool that is currently under development on our test site and exists only for internal testing purposes.

Automated Docking

Automated docking tool can be used to predict how a ligand (carbohydrate) binds to the receptor (antibody). The tool uses VINA-CARB to dock the carbohydrate to the antibody. If you would like to know details about VINA-CARB and the protocol implemented in this tool, please refer to these papers. Please note that you will also have to cite these papers if you use this tool for your work:

Nivedha, A. K.; Makeneni, S.; Foley, B. L.; Tessier, M. B.; Woods, R. J., Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff. Journal of Computational Chemistry 2014, 35, 526-539

Nivedha, A. K.; Thieker, D.; Woods, R. J., Vina-Carb: Improving glycosidic angles during carbohydrate docking. Journal of Chemical Theory and Computation (in press)

Makeneni, S.; Thieker, D.; Woods R. J., Applying pose clustering and MD simulations to eliminate false positives in molecular docking. (in preparation).

Input files/requirements

In order to use this tool, a 3D structure of the antibody in the protein data bank (PDB) format is required.

  • It is important that the pdb file contains the light chain coordinates followed by the heavy chain coordinates in that order and that they are separated by a TER card.
  • Currently, if there are multiple copies of the antibody, the tool utilizes the first copy of the antibody it identifies.

The structure of the ligand can be generated using one of the following options:

  1. Carbohydrate builder
  2. Entering a sequence
  3. Choosing a carbohydrate from the existing libraries.

In future, we intend to provide an option to upload a pdb file of the ligand as well.

Docking options

Several different docking options are provided which include flexibility of the ligand and the number of docking experiments.

Please note that if you choose flexible ligand or multiple docking experiments, it might take more than a few minutes for the docking job to finish depending on the size of the ligand. Therefore, it is important to leave your email address so we can send you a notification when the job is done. Also, we advise that you upload a unique project name for your project so we can easily access your input/output files for debugging in case there is an error.