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Protein-Protein Docking

Please upload the docked E3 ligase–small molecule complex, upload the target protein or protein-small molecule complex structure, and provide your email address. After submission, E3Docker will perform protein-protein docking and send the result notification to your email.

Docked E3 Ligase–Small Molecule Complex

Upload the docking result file of the E3 ligase bound with the small molecule ligand.

Supported format: .pdb

No file selected

Target Protein or Complex Structure

Upload the target protein structure, or a protein-small molecule complex, for protein-protein docking.

Supported format: .pdb

No file selected

Interface Residue Constraints Optional

Choose global docking, or select protein residues or bound small-molecule atoms. Small-molecule atoms are converted to nearby protein interface residues for CoDockPP.

1E3 complexClick the blue protein
2Target proteinThen click the orange protein
Upload both PDB files to start constraint selection
Drag to rotate · Scroll to zoom · Click to select a constraint point
Hover over a protein to inspect atoms
Your structures will appear here Upload both PDB files, then click a protein residue in the 3D viewer.
E3 complex Target protein Selected constraint points
1E3 Complex Residues
Waiting
No residues selected
Click a protein atom or a bound small-molecule atom
2Target Protein Residues
Next
No residues selected
Click a protein atom or a bound small-molecule atom
Constraint logic
Required atom pairs

Selected protein residues guide CoDockPP directly. A selected bound small-molecule atom is converted to nearby protein interface residues. Models are ranked by the original CoDockPP workflow, and bound small molecules remain attached to their parent proteins.

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