Protein–Ligand Quantum Docking & Binding Free Energy — Hands-on

Combine classical docking speed with quantum accuracy. Learn to generate sensible poses, apply QM-based re-scoring and QM/MM relaxation, and compute binding energies with transparent error estimates and publication-ready bundles.

Protein–Ligand Quantum Docking & Binding Free Energy

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Session Index

Session 1 — Classical → QM-Ready Poses Session 2 — QM/Semiempirical Re-scoring Session 3 — QM/MM Relaxation & ΔG Workflows Session 4 — Mini Capstone: Pose → ΔG → Report

Session 1

Fee: Rs 6300

Classical → QM-Ready Poses

Generate diverse poses and select QM candidates

Vina/Smina rDock/GOLD* RMSD clustering

Prep for QM: protonation, tautomers, charge & spin states

RDKit/Open Babel PROPKA/PDB2PQR RESP/ESP seeds

Pocket trimming and boundary masks for QM/MM boxes

shell radii link-atom plan

Session 2

Fee: Rs 8400

QM/Semiempirical Re-scoring

Fast semiempirical scoring of poses (xTB family)

GFN1/2-xTB GBSA-xTB strain/interaction split

DFT re-scoring & corrections

DFT-D3/D4 def2-SVP/TZVP BSSE (counterpoise)

Interaction decomposition for insight

SAPT (Psi4) FMO (overview)

Session 3

Fee: Rs 11200

QM/MM Relaxation & ΔG Workflows

QM/MM pose relaxation and contact sanity checks

ORCA/CP2K/Psi4 + OpenMM link atoms PLIP/LigPlot+

Binding free energy strategies with QM corrections

MM-PBSA/GBSA (+QM ΔE) alchemical FEP/TI (hybrid) BAR/MBAR

Error bars & robustness: sampling, solvation and dielectric choices

bootstraps/replicates implicit vs explicit

Session 4

Fee: Rs 14000

Mini Capstone: Pose → ΔG → Report

Pick a ligand, re-score with xTB/DFT, relax via QM/MM, and compute ΔG with uncertainty

Theory + Practical

Provenance & reproducibility (levels, configs, seeds, logs)

YAML/JSON configs workflow scripts Quarto summary

Deliverables: figures, tables, README & manifest

PDF CSV/TSV checksums

PDF

Protein–Ligand Quantum Docking & Binding Free Energy Training | xTB/DFT Re-scoring, QM/MM, ΔG with Uncertainty

Protein–Ligand Quantum Docking & Binding Free Energy — Hands-on