Skill843 repo starsupdated 4d ago

chemistry

This Claude Code skill provides computational chemistry and drug discovery workflows using tools like RDKit for molecular analysis, AutoDock Vina for protein-ligand docking, and access to databases including PubChem and ChEMBL. Use it for virtual screening of compound libraries, QSAR modeling to predict molecular properties, and molecular dynamics simulations when designing or validating potential drug candidates.

View source Repository: ScienceClaw

Install in Claude Code

Copy

git clone --depth 1 https://github.com/beita6969/ScienceClaw /tmp/chemistry && cp -r /tmp/chemistry/skills/chemistry ~/.claude/skills/chemistry

Then start a new Claude Code session; the skill loads automatically.

Definition

SKILL.md

# 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 |