Antibody Docking
Step 1: Upload Antibody and Glycan
Step 2: Choose Docking Options
Step 3: Download Files
This tool is currently being developed.

Upload Antibody 3D Structure (PDB)

Notes about Protein Uploads:
  • We currently only support PDB-formatted files (not MMCIF).
  • The file format is fairly strict. Detection of the chains depends on the chain numbering.
  • The light chain must precede the heavy chain in the PDB file.
  • There must be a TER card (a line with just TER) between the light and heavy chains.
  • Example PDBID: 1M7D is an example structure that works with DGalpa1-4DGlcpb1-OH as the antigen.
  • The example should take ~1 minute to complete unless our queue is full.
Upload Antibody PDB File (required)
   

Upload A Carbohydrate Antigen 3D Structure (PDB)

Notes about Glycan Uploads:
  • We currently only support PDB-formatted files (not MMCIF).
  • We highly recommend using glycan files generated by one of our builders.
  • PDB files generated by other means may not work.
  • The glycan must be minimized.
  • File provided by "PDB" button on any tool's Downloads step is minimized.
  • If a project is downloaded, please use "min-gas.pdb" in the provided zip file.
Upload Glycan PDB File (required)