# Chemistry

> Chemistry & Drug Discovery

- Skill: `biotender-max/chemistry` (Agent Skill)
- Install (CLI): `npx skillmds@latest add biotender-max/chemistry`
- Raw SKILL.md: https://api.skillmd.com/api/skills/biotender-max/chemistry/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Product & Planning
- Author: BioTender-max (https://skillmd.com/u/biotender-max)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/biotender-max/chemistry

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# Chemistry & Drug Discovery

## Overview
Computational chemistry, cheminformatics, and drug discovery workflows.

## Key Tools
- **RDKit**: Molecular manipulation, fingerprints, descriptors, substructure search
- **PubChem**: Chemical compound database (100M+ compounds)
- **ChEMBL**: Bioactivity database for drug-like molecules
- **Open Babel**: Format conversion, 3D generation
- **AutoDock Vina**: Molecular docking
- **GROMACS/OpenMM**: Molecular dynamics simulations

## Common Workflows

### Virtual Screening
1. Define target (protein structure from PDB)
2. Prepare compound library (from ChEMBL/ZINC/Enamine)
3. Filter by drug-likeness (Lipinski's Rule of Five)
4. Docking (AutoDock Vina, GNINA)
5. Scoring and ranking
6. ADMET prediction (absorption, distribution, metabolism, excretion, toxicity)
7. Hit validation

### QSAR Modeling
1. Curate activity data (ChEMBL IC50/Ki/EC50)
2. Calculate molecular descriptors (RDKit)
3. Feature selection
4. Model training (Random Forest, XGBoost, neural network)
5. Validation (cross-validation, external test set)
6. Applicability domain assessment

### Molecular Property Prediction
- Lipophilicity (LogP)
- Solubility (LogS)
- Permeability (PAMPA, Caco-2)
- Metabolic stability (CYP inhibition)
- hERG toxicity
- BBB penetration

## Databases
| Database | Content | Access |
|----------|---------|--------|
| PubChem | 100M+ compounds | Free API |
| ChEMBL | Bioactivity data | Free API |
| PDB | 200K+ protein structures | Free API |
| ZINC | Purchasable compounds | Free download |
| DrugBank | Drug information | Free academic |
| Materials Project | Inorganic materials | Free API |