Free Energy Methods — MM PBSA MM GBSA FEP TI AD — Hands-on

Gain hands-on experience with free energy methods used in modern drug discovery. This module covers thermodynamic foundations, MM-PBSA/MM-GBSA end point workflows, alchemical FEP/TI protocols, practical convergence checks and result interpretation so that binding energy numbers can be used more confidently in decision making.

Free Energy Methods — MM PBSA MM GBSA FEP TI AD

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Session Index

Session 1 — Free Energy & End Point Method Foundations Session 2 — MM PBSA / MM GBSA Workflows & Analysis Session 3 — Alchemical FEP / TI & Sampling Session 4 — Mini Capstone: Binding Free Energy Project

Session 1

Fee: Rs 8800

Free Energy & End Point Method Foundations

Thermodynamic background for binding free energies

ΔG ΔH ΔS interpretation partition functions and ensembles thermodynamic cycles for binding

Overview of free energy method families

end point MM PBSA / MM GBSA alchemical FEP / TI approaches pros and cons by project stage

Key ingredients: sampling, force fields and solvents

trajectory quality requirements implicit vs explicit solvent choices limitations to keep in mind

Session 2

Fee: Rs 11800

MM PBSA / MM GBSA Workflows & Analysis

MM PBSA / MM GBSA theory and decomposed terms

molecular mechanics energy components solvation and polar vs non polar parts entropy estimation options overview

Practical MM PBSA / MM GBSA setup and runs

extracting frames from MD trajectories parameter and dielectric choices batch calculations on series of ligands

Post processing, convergence and per residue insight

error bars and convergence checks per residue free energy decomposition linking results to SAR and design

Session 3

Fee: Rs 14800

Alchemical FEP / TI & Sampling Strategies

Alchemical free energy concepts and cycles

relative vs absolute binding free energies thermodynamic cycles for FEP / TI mapping transforms between ligands

Setting up FEP / TI windows and simulations

lambda schedules and soft core ideas equilibration and production lengths handling charge and topology changes

Analyzing alchemical results and diagnosing issues

BAR / MBAR analysis basics overlap and convergence indicators comparing to experiment and MM PBSA

Session 4

Fee: Rs 18800

Mini Capstone: Binding Free Energy Project

Designing a small binding free energy study

Theory + Practical

Running MM PBSA / MM GBSA and optional FEP / TI steps

protocol choice and justification numerical results with uncertainties comparison across a small ligand series

Deliverables: free energy report and design implications

spreadsheet of ΔG estimates and errors notebook or script for the workflow short slide deck for project review

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Free Energy Methods — MM-PBSA, MM-GBSA, FEP & TI Training | Binding Free Energies & Workflows

Free Energy Methods — MM PBSA MM GBSA FEP TI AD — Hands-on