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Docking for Cheminformatics: Benchmarking & Scoring | Validation-Driven, Reproducible Workflows

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Cheminformatics, QSAR & ADMET >> Docking for Cheminformatics: Benchmarking & Scoring | Validation-Driven, Reproducible Workflows

Docking for Cheminformatics — Hands-on

Learn docking the right way for discovery-scale cheminformatics. This module covers end-to-end protein/ligand preparation, search/exhaustiveness, scoring and consensus rescoring, and benchmark-driven validation (redocking, cross-docking, decoy sets) . You will generate audit-ready reports with enrichment metrics, pose QC, and reproducible configs.

Docking for Cheminformatics: Benchmarking & Scoring
Help Desk · WhatsApp
Session 1
Fee: Rs 17800
Protein & Ligand Preparation
  • Target structure curation
    • chain/altloc selection protonation/tautomers (pH) cofactors/metal handling
  • Binding site definition
    • reference ligand/box cavity detection conserved waters
  • Ligand prep & QC
    • enumeration (stereo/proto) 3D conformers (ETKDG) strain/flags & PAINS
Session 2
Fee: Rs 20800
Docking Protocols & Parameters
  • Search/exhaustiveness & sampling
    • genetic/local search pose clustering constraints & pharmacophores
  • Protein flexibility & waters
    • soft/induced-fit options key waters retained metal constraints
  • Workflow hygiene
    • determinism/seeds runtime/caching checkpoint/resume
Session 3
Fee: Rs 23800
Scoring, Consensus & Benchmarking
  • Scoring families & rescoring
    • empirical/knowledge-based consensus/rank fusion MM/GBSA-lite checks
  • Benchmark design & metrics
    • redocking/cross-docking decoys (DUD-E-style) ROC/PR, EF@1%, BEDROC
  • Pose QC & filters
    • strain/contacts clashes interaction fingerprints synthetic feasibility flags
Session 4
Fee: Rs 27800
Mini Capstone: Docking Benchmark Report
  • Design a benchmark (target + decoys) & execute docking
    • Theory + Practical
  • Analyze enrichment & pose quality
    • ROC/PR & EF curves IFP/contacts summary consensus ranking
  • Deliverables
    • ranked hit list + poses benchmark report (PDF/HTML) reproducible configs/notebooks


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