What can this MCP do with docking poses?

It evaluates binding affinity, identifies chemical bonds, maps contact residues, and ranks different docking configurations.

Does it account for solvation in energy calculations?

Yes, the get_binding_energy capability includes solvation and entropy effects in its total affinity calculation.

Which AI clients can I use with this MCP?

You can use any MCP-compatible client, such as Claude, Cursor, Windsurf, or VS Code.

How does it identify chemical bonds?

The analyze_interactions capability identifies and categorizes specific bonds like hydrogen bonds and salt bridges.

Can I use this to find the best binding mode?

Yes, the compare_poses capability is designed to rank multiple configurations to find the most stable mode.

How do I calculate the total binding affinity?

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

Can I see which amino acids are interacting with my ligand?

Yes, the identify_binding_site capability maps the specific protein residues in immediate proximity to the ligand based on a distance threshold.

How can I find the most stable docking configuration?

Use the compare_poses capability with a list of poseIds to rank multiple configurations and identify the best binding mode.

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Connect Protein-Ligand Docking Score to ChatGPT and Claude

Set it up once and it works in ChatGPT, Claude, Cursor, and any other client you love. It all runs safely in the background, so you can relax and focus on what really matters. Get precise binding affinity and interaction data from docking poses.

Ask AI about this Connector

Developed, maintained, and hosted by Vinkius.

MCP VERIFIED · PRODUCTION READY · VINKIUS GUARANTEED

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Works with modern AI clients that support MCP, including ChatGPT, Claude, Cursor, and more.

Your AI does the work. We keep it safe and sound.

No other AI tool gives you this. Your workflow runs in the client you already love, your account stays protected, and you decide what the agent can and cannot do. It is the whole reason to make the switch.

Each Connector lives inside our infrastructure, the same place where your workflow runs. The three things below are already part of it, working quietly in the background so you never have to think about them. Nothing to add, nothing to set up, nothing to worry about.

V8 Isolate01

Each Connector runs inside its own sealed environment.

Each Connector runs inside its own sealed V8 runtime — no access to your files, your system, or other servers. A Connector never sees past its own request.

Kill Switch02

One switch stops every agent. Instantly.

One action deactivates every Connector, revokes every token, and ends every session at once. AI Governance keeps the record.

FinOps per User03

Spending limits that pause instead of surprise.

Every user keeps their own connections and credentials, isolated from everyone else. Anything that would cross your spending limit is held for your approval, not billed.

Three controls, built into the layer your AI connects through.

Curated set · 4 capabilities

We ship only the actions that matter.

Capability set01 / 01

01-04

4 capabilities in this set.

Part of 4 available through Protein-Ligand Docking Score.

01
Compare poses
This capability compares different docking configurations. It helps you find which pose represents the most stable binding mode.
02
Get binding energy
This capability calculates the total estimated binding affinity for a specific pose. It accounts for factors like solvation and entropy.
03
Identify binding site
This capability maps the protein residues in immediate proximity to the ligand. It identifies exactly which parts of the protein are touching the molecule.
04
Analyze interactions
This capability categorizes the chemical bonds formed between the ligand and the protein. It identifies specific interactions like hydrogen bonds or salt bridges.

Real work

What teams actually run

Lead Optimization

Compare different ligand modifications to see which one produces the most stable binding energy.

Binding Site Characterization

Identify the specific residues that form salt bridges or hydrogen bonds with a new drug candidate.

Docking Pose Validation

Rank a set of generated docking poses to determine the most likely binding mode.

Interaction Profiling

Quickly get a list of all residues in the immediate vicinity of a ligand.

One connector, every AI

Protein-Ligand Docking Score works with the most popular AI clients.

These are the most popular clients, each with a step-by-step guide: one link, set up once, with governance and visibility built in. And because everything runs on the MCP standard, the same connection also works in any other compatible client — nothing to rebuild.

Building your own app? The connector is yours to use.

You don't need a client to put Protein-Ligand Docking Score to work: the same hosted connection plugs into your own applications and agent code, with the same governance on every request. Build with it, chat with it — one connection for both.

Observed, not estimated

875ms average. Fast in production.

Protein-Ligand Docking Score is checked daily against the live service.

Daily averagePeak 1051ms

Oct 3Today

Fastest day: 787ms
Slowest day: 1051ms
14-day trend: Improving-7%

Connect your client

One URL. Every client.

Activate the Connector, copy your link, and paste it into the client you already use. 4 capabilities arrive ready to run.

Preview access · not provider authentication

The vk_preview_* token belongs to Vinkius preview infrastructure. It lets Claude discover and display the capabilities of Protein-Ligand Docking Score, so you can see the experience inside your AI.

It does not authenticate your account with Protein-Ligand Docking Score. Actions requiring credentials or live account data may not run until you activate the Connector and authorize the service.

Protein-Ligand Docking Score Connector

You're all set. Choose your MCP client and follow the setup instructions.

Connector linkhttps://edge.vinkius.com/vk_preview_ciuUzOG1Qnl6b5M4bg8GJvku5vmnaipFWSX2VIUv/mcp

Claude Desktop

Follow the steps below to connect in seconds.

1In Claude Desktop, open Settings → Connectors.
2Click “Add custom connector” and paste the connector link above as the remote MCP server URL.
3Click Add and start a new chat — Protein-Ligand Docking Score capabilities are ready to use.

Configuration · claude_desktop_config.jsonCopy

{
  "mcpServers": {
    "protein-ligand-docking-score-mcp": {
      "url": "https://edge.vinkius.com/vk_preview_ciuUzOG1Qnl6b5M4bg8GJvku5vmnaipFWSX2VIUv/mcp"
    }
  }
}

Claude
ChatGPT
Cursor
VS Code
Windsurf
Claude Code
JetBrains
Cline

Step-by-step instructions for each client are in the guide. How to connect

Guided setup for Claude? Set up Protein-Ligand Docking Score in Claude and other AIs

See all the AI clients this connector works with ↑

Who it's for

Built for the work Protein-Ligand Docking Score owners hand off.

This MCP is built for researchers working in computational chemistry and drug discovery.

01
Computational Chemists
They use the AI to quickly summarize docking results and interaction profiles.
02
Drug Discovery Researchers
They hand off docking pose data to the AI to rank potential lead compounds.
03
Structural Biologists
They use the capability to identify contact residues and binding site characteristics.

FAQ

Questions Protein-Ligand Docking Score owners ask.

01
What can this MCP do with docking poses?
It evaluates binding affinity, identifies chemical bonds, maps contact residues, and ranks different docking configurations.
02
Does it account for solvation in energy calculations?
Yes, the get_binding_energy capability includes solvation and entropy effects in its total affinity calculation.
03
Which AI clients can I use with this MCP?
You can use any MCP-compatible client, such as Claude, Cursor, Windsurf, or VS Code.
04
How does it identify chemical bonds?
The analyze_interactions capability identifies and categorizes specific bonds like hydrogen bonds and salt bridges.
05
Can I use this to find the best binding mode?
Yes, the compare_poses capability is designed to rank multiple configurations to find the most stable mode.
06
How do I calculate the total binding affinity?
You can use the get_binding_energy capability by providing a valid poseId. You can also optionally include solvation and entropy effects in the calculation.
07
Can I see which amino acids are interacting with my ligand?
Yes, the identify_binding_site capability maps the specific protein residues in immediate proximity to the ligand based on a distance threshold.
08
How can I find the most stable docking configuration?
Use the compare_poses capability with a list of poseIds to rank multiple configurations and identify the best binding mode.

Explore

More in Chemistry

Connect Protein-Ligand Docking Score to Claude, Cursor, ChatGPT & more

Your AI does the work. We keep it safe and sound.

Each Connector runs inside its own sealed environment.

One switch stops every agent. Instantly.

Spending limits that pause instead of surprise.

We ship only the actions that matter.

01-04

Compare poses

Get binding energy

Identify binding site

Analyze interactions

What teams actually run

Lead Optimization

Binding Site Characterization

Docking Pose Validation

Interaction Profiling

Building your own app? The connector is yours to use.

Protein-Ligand Docking Score Connector

Claude Desktop

Computational Chemists

Drug Discovery Researchers

Structural Biologists

What can this MCP do with docking poses?

Does it account for solvation in energy calculations?

Which AI clients can I use with this MCP?

How does it identify chemical bonds?

Can I use this to find the best binding mode?

How do I calculate the total binding affinity?

Can I see which amino acids are interacting with my ligand?

How can I find the most stable docking configuration?

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