MCP For Claude Marketplace
Protein-Ligand Docking Score

Protein-Ligand Docking Score MCP Connector for Claude

A+

Evaluates protein-ligand binding affinity and interaction characteristics from docking poses.

4 tools Official Updated Oct 1, 2026 Official Vinkius Partner
More Details Connect to Claude

This MCP server provides specialized tools for analyzing the thermodynamic stability and chemical interactions of protein-ligand complexes. Use get_binding_energy to calculate total affinity, including solvation and entropy effects. Use analyze_interactions to identify specific chemical bonds like Hydrogen Bonds or Salt Bridges. You can also use identify_binding_site to map contact residues or compare_poses to rank multiple docking configurations for the most stable binding mode.

dockingproteinligandbinding-affinitymolecular-dynamics

4 tools expose this connector's capabilities to your AI agent.

compare_poses

Compares multiple docking configurations to find the most stable binding mode

get_binding_energy

Calculates the total estimated binding affinity for a specific docking pose

identify_binding_site

Maps the specific protein residues that are in immediate proximity to the ligand

analyze_interactions

Identifies and categorizes the types of chemical bonds formed between the ligand and the protein

See how to talk to your AI agent using Protein-Ligand Docking Score.

What is the binding energy for pose 'pose_001' including solvation?

The total binding energy for pose 'pose_001' is -8.4 kcal/mol, which includes a solvation contribution of -1.2 kcal/mol.

Which residues are in contact with the ligand in pose 'pose_abc'?

The ligand is in contact with residues HIS-42, TRP-105, and ASP-12 in pose 'pose_abc'.

Compare the stability of poses 'p1', 'p2', and 'p3'.

The best pose is 'p2' with a binding energy of -9.2 kcal/mol. The energy difference between 'p2' and the next best pose is 0.5 kcal/mol.

You can use the `get_binding_energy` tool by providing a valid `poseId`. You can also optionally include solvation and entropy effects in the calculation.

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