Binding Free Energy — MM-PBSA & MM-GBSA — Hands-on

Learn how to estimate binding free energies from molecular dynamics trajectories using MM-PBSA and MM-GBSA end point methods. This module covers theory, system and trajectory preparation, running MM-PBSA/MM-GBSA calculations, per residue decomposition, uncertainty analysis and practical interpretation so that you can use these approaches realistically in discovery and mechanistic projects.

Binding Free Energy — MM-PBSA & MM-GBSA

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Session Index

Session 1 — Theory & End Point Free Energy Methods Session 2 — Trajectory & Snapshot Preparation Session 3 — MM-PBSA/MM-GBSA Runs & Decomposition Session 4 — Interpretation, Uncertainty & Reporting

Session 1

Fee: Rs 8800

Theory & End Point Free Energy Methods

Thermodynamics of binding and free energy cycles

ΔG binding, enthalpy and entropy standard state corrections connection to K_d and IC₅₀

End point vs alchemical and pathway methods

MM-PBSA and MM-GBSA concepts assumptions and approximations use cases and limitations

Energy components in MM-PBSA/MM-GBSA

molecular mechanics term polar and non polar solvation entropy estimation options overview

Session 2

Fee: Rs 11800

Trajectory & Snapshot Preparation

Using MD trajectories for MM-PBSA/MM-GBSA

equilibration and production checks periodic boundary and imaging issues choosing time windows

Preparing topologies for complex, receptor and ligand

consistent force field parameters stripping solvent and ions for analysis handling cofactors and metals

Snapshot selection and convergence considerations

sampling frequency and number of frames block averaging ideas quick diagnostics before production runs

Session 3

Fee: Rs 14800

MM-PBSA/MM-GBSA Runs & Decomposition

Running MM-PBSA/MM-GBSA calculations

setting dielectric and solvent parameters polar vs non polar contributions parallelisation and performance tips

Per residue and per group energy decomposition

mapping hot spots on the structure side chain vs backbone contributions support for mutagenesis hypotheses

Entropy estimation options and trade offs

normal mode vs quasi harmonic approaches computational cost vs accuracy when relative trends are sufficient

Session 4

Fee: Rs 18800

Interpretation, Uncertainty & Reporting

Interpreting ΔG values and series ranking

Theory + Practical

Uncertainty, error bars and comparison to experiment

block analysis and bootstrapping correlation with assay data identifying systematic bias

Best practices, integration with docking/FEP and reporting

when to trust relative trends combining MM-PBSA/MM-GBSA with other methods figure panels and methods text for manuscripts

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Binding Free Energy MM-PBSA & MM-GBSA Training | End-Point Binding Affinity from MD

Binding Free Energy — MM-PBSA & MM-GBSA — Hands-on