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Pharmacophore Modeling: Hypothesis Generation & Screening | Validation & Enrichment-focused

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Cheminformatics, QSAR & ADMET >> Pharmacophore Modeling: Hypothesis Generation & Screening | Validation & Enrichment-focused

Pharmacophore Modeling — Hands-on

Create actionable pharmacophore models that capture the essential interaction patterns driving activity. In this hands-on module you will derive hypotheses from aligned actives and protein–ligand contacts, validate with decoys, and execute ligand-based virtual screening workflows with robust enrichment and triage practices.

Pharmacophore Modeling: Hypothesis Generation & Screening
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Session 1
Fee: Rs 15800
Concepts, Features & Hypothesis Building
  • Pharmacophore basics & SAR inputs
  • essential vs optional features exclusion volumes feature tolerance/radii
  • Feature perception & types
  • HBD/HBA aromatic/hydrophobe pos/neg ionizable
  • Tooling & workflow setup
  • RDKit/Pharmit Open3DAlign/Align-it PLIP for contacts
Session 2
Fee: Rs 18800
Alignment, Constraints & Validation
  • Active set alignment & hypothesis generation
  • shape/pharmacophore/MCS multi-conformer handling constraints & optionality
  • Hypothesis scoring & pruning
  • coverage & selectivity RMSD/tolerances pose sanity checks
  • Validation with decoys
  • DUD-E style decoys ROC-AUC/EF1% early enrichment metrics
Session 3
Fee: Rs 21800
Virtual Screening & Hit Triage
  • Database prep & multi-conformer libraries
  • enumeration & protonation ETKDG conformers diversity curation
  • Search & ranking
  • pharmacophore fit score shape/3D similarity rescoring & filters (PAINS/Lipinski)
  • Triage & follow-up
  • clustering & representative picks basic docking cross-check synthetic feasibility notes
Session 4
Fee: Rs 25800
Mini Capstone: Enrichment Workflow
  • Build & validate a hypothesis, then screen
  • Theory + Practical
  • Measure enrichment & report
  • ROC/PR & EF curves top-N precision reproducible configs
  • Deliverables
  • pharmacophore model file ranked hit list + clusters enrichment report & notebook/script


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