DiffDock Automated Protein-Ligand Docking
Note:
- Local files are not directly accessible by the server. Please upload them to the server using
molclaw-file-transferbefore execution. - For PDB file inputs, it is recommended to preprocess them using
molclaw-pdbfixerbefore execution. - Please refer to skill
molclaw-scp-serverto complete tool invocation.
⚠ TOOL NOT AVAILABLE: The
diffdock_autotool is not currently deployed on the MCP server. The DiffDock API endpoint is disabled. Do NOT attempt to calldiffdock_auto. Use one of these alternatives instead:
molecule_docking_quickvina_fullprocess— GPU-accelerated AutoDock Vina variant (see skillmolclaw-quickvina-docking)karmadock_tool— ML-based docking (see skillmolclaw-karmadock-tool)