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Foundations of Cheminformatics & Molecular Representations (SMILES/InChI) | Hands-on with RDKit & Open Babel

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Cheminformatics, QSAR & ADMET >> Foundations of Cheminformatics & Molecular Representations (SMILES/InChI) | Hands-on with RDKit & Open Babel

Foundations of Cheminformatics & Molecular Representations — Hands-on

Build a rock-solid foundation in cheminformatics by learning how molecules are represented, validated, standardized, and exchanged across tools and pipelines. You will work hands-on with RDKit and Open Babel to parse, sanitize, canonicalize, and export structures in industry-standard formats with best practices for reproducibility.

Foundations of Cheminformatics & Molecular Representations (SMILES/InChI)
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Session 1
Fee: Rs 9800
SMILES, InChI & Stereochemistry
  • SMILES fundamentals & tokens
  • rings & branches aromaticity models charges & isotopes
  • InChI & InChIKey
  • layers & normalization use in de-duplication identifier hygiene
  • Stereochemistry
  • R/S, E/Z @ / @@ in SMILES double bond stereo
Session 2
Fee: Rs 12800
File Formats, Parsing & Sanitization
  • Exchange formats & interop
  • SDF / MOL / MOL2 SMI / CSV PDBQT basics
  • RDKit & Open Babel toolchain
  • parsing & sanitization valence/kekulization error handling
  • Metadata & properties
  • SDF data fields round-tripping SMILES canonical vs. input
Session 3
Fee: Rs 15800
Canonicalization & Standardization
  • Canonical SMILES & uniqueness
  • hashing & IDs tautomers & protonation salt/solvent stripping
  • Normalization workflows
  • neutralization aromaticity model choice standard tautomers
  • InChI/InChIKey in pipelines
  • de-dup & merge cross-database linking identifier QA/QC
Session 4
Fee: Rs 19800
Mini Capstone: Library Curation
  • Curate a vendor/HTS library
  • Theory + Practical
  • Deduplicate, standardize & export
  • InChIKey de-dup descriptor precompute SDF/SMI/CSV deliverables
  • Deliverables: standardized set & report
  • QA/QC checklist pipeline script/notebook method notes


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