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chemistry

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962
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Science
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MIT
Last commit
Oct 8, 2026

skills/chemistry/SKILL.md

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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

DatabaseContentAccess
PubChem100M+ compoundsFree API
ChEMBLBioactivity dataFree API
PDB200K+ protein structuresFree API
ZINCPurchasable compoundsFree download
DrugBankDrug informationFree academic
Materials ProjectInorganic materialsFree API

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