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OpenBio provides computational chemistry tools for analyzing molecules, calculating properties, and assessing drug-likeness.

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RDKit - Chemical Informatics

Purpose: Comprehensive molecular analysis and property calculation Available analyses:
  • Calculate molecular properties (MW, logP, HBD/HBA, TPSA)
  • Assess drug-likeness (Lipinski, Veber rules)
  • Generate 2D structure visualizations
  • Convert between formats (SMILES, InChI)
  • Find substructures and functional groups
  • Calculate molecular similarity
  • Generate chemical fingerprints
Example: “Calculate properties for this SMILES: CC(=O)Oc1ccccc1C(=O)O”

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SA Score - Synthetic Accessibility

Purpose: Predict ease of chemical synthesis Features:
  • Scale: 1-10 (1 = easy, 10 = very difficult)
  • Prioritizes synthesizable compounds
  • Filters virtual libraries
  • Guides medicinal chemistry design
Interpretation:
  • 1-3: Easy, routine synthesis
  • 4-6: Moderate difficulty, feasible
  • 7-8: Difficult, requires expertise
  • 9-10: Very difficult or impractical

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Quick Examples

  • “Calculate properties for this SMILES: CC(=O)Oc1ccccc1C(=O)O”
  • “Check if this compound is drug-like”
  • “Show the structure of aspirin”
  • “Calculate synthetic accessibility for this compound”
  • “How similar are compound A and B?”

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Common Workflows

Compound Characterization: Calculate properties → Check drug-likeness → Assess synthesis → Generate report Library Filtering: Filter by MW → Filter by logP → Check Lipinski → Calculate SA score → Rank results Similarity Search: Generate fingerprint → Calculate similarity → Rank by Tanimoto → Compare structures