Koskamo

cmxflow MCP

A composable cheminformatics workflow framework that allows LLM agents to build and optimize molecular pipelines. It supports ligand preparation, clustering, docking, and virtual screening using Bayesian optimization to tune parameters for tasks like similarity search and enrichment.

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

cmxflow MCP logo, by b-shieldsCommunity listingLocal stdioSource reviewed; not executedPublished by b-shields
Vendor documentation

What you can do with it

  • Build ligand-based virtual screening workflows
  • Optimize molecular docking parameters
  • Prepare ligands for docking via standardization and ionization
  • Cluster molecules using 2D or 3D similarity metrics

Source and maintenance

Community listingRegistry 0.4.0
mcp-registry: io.github.b-shields/cmxflow@0.4.0Source repositoryProject website
Maintenance checked

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

cmxflow 0.4.0

pypiuvx
cmxflow package definition
{
  "version": "0.4.0",
  "transport": "stdio",
  "identifier": "cmxflow",
  "runtimeHint": "uvx",
  "registryType": "pypi",
  "runtimeArguments": [
    {
      "type": "positional",
      "value": "--from"
    },
    {
      "type": "positional",
      "value": "cmxflow"
    },
    {
      "type": "positional",
      "value": "cmxflow-mcp"
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

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Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "cmxflow-mcp": {
      "command": "uvx",
      "args": [
        "cmxflow==0.4.0"
      ]
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "cmxflow-mcp": {
      "command": "uvx",
      "args": [
        "cmxflow==0.4.0"
      ]
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.
VS Code configuration
{
  "servers": {
    "cmxflow-mcp": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "cmxflow==0.4.0"
      ]
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.
Claude Desktop configuration
{
  "mcpServers": {
    "cmxflow-mcp": {
      "command": "uvx",
      "args": [
        "cmxflow==0.4.0"
      ]
    }
  }
}

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