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Free Energy Calculations & Binding Affinity Training | MM-PBSA/GBSA, Alchemical FEP/TI, WHAM/PMF, Uncertainty

Compute binding affinities with rigor: MM-PBSA/GBSA, alchemical FEP/TI with soft-core potentials, umbrella sampling/PMF, error bars (BAR/MBAR/bootstraps) , and reproducible affinity reports.

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Proteomics, Structural Bioinformatics, Molecular Modeling

Free Energy Calculations & Binding Affinity — Hands-on

From quick end-state estimates to rigorous alchemical workflows: set up, run, and analyze binding free energy calculations with best practices for convergence, uncertainty, and transparent reporting.

Free Energy Calculations & Binding Affinity (MM-PBSA, FEP)
Help Desk · WhatsApp
Session 1
Fee: Rs 6300
MM-PBSA/GBSA: Theory & Setup
  • End-state methods, dielectric models and entropy options
    • Theory
  • Running MM-PBSA/GBSA on MD snapshots
    • gmx_MMPBSA MMPBSA.py (AMBER) trajectory subsampling
  • Interpreting components & sanity checks
    • ΔEMM, ΔGsolv, TΔS per-residue decomposition
Session 2
Fee: Rs 8400
Alchemical FEP/TI Workflows
  • λ-schedules, soft-core potentials, restraints & standard states
    • Boresch restraints standard-state correction decoupling schemes
  • Tooling & engines (overview)
    • GROMACS+PLUMED OpenMM/pmx AMBER TI FEP+*
  • Analysis: TI/BAR/MBAR and error propagation
    • BAR/MBAR overlap matrices CI/bootstraps
Session 3
Fee: Rs 11200
Convergence, Errors & Enhanced Sampling
  • Convergence diagnostics & window overlap checks
    • time-series decorrelation effective sample size replicates
  • Umbrella sampling & PMF with WHAM
    • reaction coordinates biasing & windows WHAM
  • Enhanced sampling (overview)
    • REST2/HREX metadynamics (PLUMED)
Session 4
Fee: Rs 14000
Mini Capstone: Affinity Report
  • Compute ΔG with MM-PBSA and a small FEP/TI example; compare vs literature
    • Theory + Practical
  • Uncertainties, convergence plots & reproducibility checklist
    • BAR/MBAR tables overlap matrices protocol YAML/inputs
  • Deliverables: figures, tables, README & manifest
    • PDF CSV/TSV checksums