Molecular Docking & Energy Minimization Techniques Training | Vina/Smina, rDock/GOLD, Rescoring & Relaxation

Prepare proteins/ligands, build grids, dock with Vina/Smina/GOLD/rDock, apply constraints, rescore, and minimize poses (MMFF/UFF/GAFF, OpenMM/GROMACS) to produce defensible, publication-ready results.

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

Molecular Docking & Energy Minimization Techniques — Hands-on

Practical docking from target prep to minimized poses. Learn clean receptor/ligand preparation, grid/box design, rigid vs flexible docking, constraints, consensus rescoring, and fast energy minimization for better pose quality and figures.

Molecular Docking & Energy Minimization Techniques

Help Desk · WhatsApp

Session Index

Session 1 — Prep: Receptor & Ligands Session 2 — Docking: Rigid/Flexible & Constraints Session 3 — Rescoring & Energy Minimization Session 4 — Mini Capstone: Dock → Minimize → Report

Session 1

Fee: Rs 6300

Preparation: Receptor & Ligands

Receptor clean-up, protonation and pocket definition

pdbfixer PDB2PQR/propka fpocket grid/box setup

Ligand standardization: stereochemistry, tautomers, charges

RDKit Open Babel Gasteiger/AM1-BCC

Cofactors, waters and metal handling; restraints & exclusions

keep/remove rules pharmacophore hints

Session 2

Fee: Rs 8400

Docking: Rigid/Flexible & Constraints

Search algorithms, parameters and reproducibility settings

AutoDock Vina/Smina rDock GOLD* exhaustiveness/seeds

Flexible side chains & induced fit strategies (overview)

rotamer sampling soft potentials constraints (HB/metal)

Pose clustering and diversity control for top-N selection

RMSD-based clusters centroid representatives

Session 3

Fee: Rs 11200

Rescoring & Energy Minimization

Consensus scoring and contact-based sanity checks

Vina/GOLD/rDock scores PLIP fingerprints strain flags

Pose relaxation and quick minimization pipelines

MMFF94/UFF/GAFF OpenMM GROMACS (steepest/CG)

Exporting scenes, tables and 2D diagrams

PyMOL/ChimeraX LigPlot+ CSV/TSV bundles

Session 4

Fee: Rs 14000

Mini Capstone: Dock → Minimize → Report

Dock a small set, relax top poses, and assemble a report bundle

Theory + Practical

Provenance, parameter files and reproducibility checklist

YAML/JSON configs Conda/Mamba Quarto

Deliverables: figures, tables, README & manifest

PDF CSV/TSV checksums