Molecular Docking Benchmarking & Validation Studies — Hands-on

Build trustworthy docking benchmarks and validation reports. Learn dataset curation, unbiased splits, proper metrics, statistical testing, and transparent reporting. Run multi-engine comparisons and summarize performance with reproducible evidence.

Molecular Docking Benchmarking & Validation Studies

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Session Index

Session 1 — Benchmark Design & Datasets Session 2 — Metrics: Ranking & Poses Session 3 — Bias, Stats & Reproducibility Session 4 — Mini Capstone: Build & Defend a Benchmark

Session 1

Fee: Rs 6300

Benchmark Design & Datasets

Choosing targets and actives/decoys; leakage and analog bias control

DUD-E DEKOIS PDBbind

Chemistry hygiene: tautomers/protomers, duplicates & data standardization

RDKit charge states salt stripping

Protein prep, grids & binding site definition

cofactors/waters box size/centers

Session 2

Fee: Rs 8400

Metrics: Ranking & Poses

Virtual screening metrics & interpretation

ROC-AUC/PR-AUC EF@1/5/10% BEDROC/RIE

Pose prediction metrics & success criteria

RMSD ≤ 2.0 Å top-n success interaction recovery

Engines & consensus scoring (overview)

Vina/Smina rDock GOLD*/Glide*

Session 3

Fee: Rs 11200

Bias, Stats & Reproducibility

Split strategies & bias checks

scaffold/time-split property-matched decoys Y-randomization

Statistical testing & uncertainty

bootstrap CI DeLong for AUC paired tests

Reproducible reports & provenance

configs/seeds/logs Snakemake/Nextflow Quarto

Session 4

Fee: Rs 14000

Mini Capstone: Build & Defend a Benchmark

Create a target-specific set, run multi-engine VS, and compute ranking/pose metrics with CIs

Theory + Practical

Consensus/score fusion & sensitivity analyses

rank aggregation threshold sweeps

Deliverables: figures, tables, README & manifest

PDF CSV/TSV checksums

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Molecular Docking Benchmarking & Validation Studies Training | Fair Datasets, Robust Metrics & Reproducible Reports

Molecular Docking Benchmarking & Validation Studies — Hands-on