# Biomolecule Modeling MCP Server

> Use this tool when you need to prepare biomolecular structures for simulation, as it cleans PDB structures and performs initial energy relaxation, providing a structured workflow for molecular dynamics and coarse-graining pipelines with input PDB files and output relaxed structures. It solves problems related to structure preparation and energy minimization, streamlining the modeling process. Ideal for use in biomolecular modeling and simulation contexts, it accepts PDB files as input and produces cleaned and relaxed structures as output.

Canonical page: https://skillsregistry.net/skills/huangjianhuster-biomolecule-modeling-mcp  
JSON: https://api.skillsregistry.net/v1/skills/huangjianhuster-biomolecule-modeling-mcp

## Description

Enables AI assistants to clean PDB structures and run initial-stage energy relaxation for biomolecular modeling. It provides a structured workflow for preparing structures before production molecular dynamics or coarse-graining pipelines.

## Trust

- **Trust score (0–1):** 1.00
- **Verification tier:** verified
- **Last scanned:** 2026-09-19

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** devops-ci
- **Updated:** 2026-09-19

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/plgkw2rnfq)
- **Repository:** <https://github.com/huangjianhuster/biomolecule-modeling-mcp>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "huangjianhuster-biomolecule-modeling-mcp"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/huangjianhuster-biomolecule-modeling-mcp` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/huangjianhuster-biomolecule-modeling-mcp/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt