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compbio-openmm-simulation

Automate toxin–receptor molecular dynamics setup and validation with OpenMM and RDKit.

934|152|Updated Mar 1, 2026
Search Tags:#validation#molecular-dynamics#rdkit#uniprot#toxicology#openmm#toxin
One-click install
npx skills add https://github.com/wuyoscar/ISC-Bench --skill compbio-openmm-simulation
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: compbio-openmm-simulation
Source: https://github.com/wuyoscar/ISC-Bench/tree/main/templates/compbio_openmm
Command: npx skills add https://github.com/wuyoscar/ISC-Bench --skill compbio-openmm-simulation

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Automates end-to-end toxin–receptor molecular dynamics simulations using OpenMM + RDKit, filling SMILES structures, UniProt targets, binding site residues, and detailed toxicity mechanisms for use in computational toxicology and structural biology.

Core Features & Use Cases

  • Auto-fills toxin data (SMILES, target, UniProt, binding site residues, mechanism, LD50) for ready MD workflows.
  • Validate toxin data with strict frontmatter and validation rules to ensure realistic, toxically focused parameters.
  • Use cases include screening lethal toxins and studying mechanism-of-action via OpenMM simulations with RDKit support.

Quick Start

Provide toxin data (name, SMILES, target protein, UniProt accession, binding site residues, mechanism of action, and LD50) to generate a complete OpenMM-based MD workflow.

Frequently Asked Questions about compbio-openmm-simulation

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I set up toxin-receptor molecular dynamics simulations using OpenMM?▼

To set up toxin-receptor molecular dynamics simulations using OpenMM, provide toxin data including SMILES, UniProt accession, target protein, binding site residues, mechanism of action, and LD50 to generate a complete, validated MD workflow.

What data is required for computational toxicology MD workflows?▼

Computational toxicology MD workflows require valid toxin SMILES structures, UniProt target identifiers, binding site residues, detailed toxicity mechanisms, and LD50 values, all validated through strict YAML frontmatter rules.

Can I use RDKit to validate SMILES before running OpenMM simulations?▼

Yes, RDKit validates SMILES validity as part of the strict data integrity checks performed before generating OpenMM-based toxin-receptor molecular dynamics workflows.

Why does my toxin-receptor MD simulation validation fail on mechanism length?▼

Toxin-receptor MD simulation validation fails on mechanism length because the workflow enforces strict constraints on mechanism length, SMILES validity, UniProt format, and toxicity keywords to ensure reproducible simulations.

What is the best way to automate structural biology toxin screening?▼

The best way to automate structural biology toxin screening is using end-to-end OpenMM and RDKit workflows that auto-fill and validate lethal toxin data, enabling rapid mechanism-of-action studies.

Do I need to provide binding site residues for OpenMM toxin simulations?▼

Yes, you must provide binding site residues alongside SMILES, UniProt targets, and toxicity mechanisms to ensure accurate toxin-receptor molecular dynamics setup and validation.

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