Protein-Protein Docking

Trial Version

Automatic protein 3D complex prediction based on two unbound 3D protein structures.

More information can be found here:

Protein-Protein Docking by Shape-Complementarity and Property Matching, Submitted

If you encounter any errors, or are interested in discussing a protein complex you work with, do not hesitate to contact Tim Geppert.

The ten best ranked complex structures will be returned to you after you hit submission


Input files for ProBinder Programm Package:

Two Protein Structures for docking in PDB file format (only .pdb is supported).

For both structures the corresponding PDB2PQR file (only .pdb is supported).

-> Get PDB2PQR to create your PDB2PQR files here

Use PDB2PQR with --chain --ff=CHARMM options.

Specify the two chains as they are annotated in the PDB and PQR files.

Specify one residue for each Protein that is involved in the interaction.

Submission form

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Upload Protein A

Upload Protein A PDBtoPQR File

Chain(s) of Protein A

Residue ID

Upload Protein B

Upload Protein B PDBtoPQR File

Chain(s) of Protein B

Residue ID