# Protein-Ligand Docking Score AI Agent Connect

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

## Overview
- **Category:** chemistry
- **Price:** Free
- **Endpoint:** https://edge.vinkius.com/vk_preview_ciuUzOG1Qnl6b5M4bg8GJvku5vmnaipFWSX2VIUv/ai-agent-connect
- **Tags:** docking, protein, ligand, binding-affinity, molecular-dynamics

## Description

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.

## Tools

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

### 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

## Prompt Examples

**Prompt:** 
```
What is the binding energy for pose 'pose_001' including solvation?
```

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

**Prompt:** 
```
Which residues are in contact with the ligand in pose 'pose_abc'?
```

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

**Prompt:** 
```
Compare the stability of poses 'p1', 'p2', and 'p3'.
```

**Response:** 
```
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.
```

## Frequently Asked Questions

**How do I calculate the total binding affinity?**
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.

**Can I see which amino acids are interacting with my ligand?**
Yes, the `identify_binding_site` tool 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` tool with a list of `poseIds` to rank multiple configurations and identify the best binding mode.