Zaoqu-Liu/skills/chemistry
skills/chemistry/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 ###
$ install --global
skillsauthnpx skillsauth add Zaoqu-Liu/ScienceClaw skills/chemistryInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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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
- Define target (protein structure from PDB)
- Prepare compound library (from ChEMBL/ZINC/Enamine)
- Filter by drug-likeness (Lipinski's Rule of Five)
- Docking (AutoDock Vina, GNINA)
- Scoring and ranking
- ADMET prediction (absorption, distribution, metabolism, excretion, toxicity)
- Hit validation
QSAR Modeling
- Curate activity data (ChEMBL IC50/Ki/EC50)
- Calculate molecular descriptors (RDKit)
- Feature selection
- Model training (Random Forest, XGBoost, neural network)
- Validation (cross-validation, external test set)
- 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 |
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