Structure Validation — Ramachandran, Geometry & Energetics — Hands-on

Learn how to rigorously validate protein structures using Ramachandran statistics, backbone and sidechain geometry, steric clashes and energy-based metrics. This module takes you from raw PDB models to fully checked, documented, and simulation-ready structures with clear validation reports suitable for publications and downstream design.

Structure Validation — Ramachandran, Geometry & Energetics

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Session Index

Session 1 — Ramachandran Plots & Backbone Geometry Session 2 — Sidechains, Rotamers & Steric Clashes Session 3 — Energetics, Force Fields & Stability Checks Session 4 — Integrated Validation Workflow & Reporting

Session 1

Fee: Rs 14800

Ramachandran Plots & Backbone Geometry

Backbone torsion angles and secondary structure

φ/ψ angles α-helix / β-sheet / loop regions cis/trans peptide bonds

Reading and interpreting Ramachandran plots

favored / allowed / disallowed regions Gly / Pro / pre-Pro special cases outlier classification

Backbone geometry validation toolkit

MolProbity / PROCHECK Phenix validation integration with PyMOL / ChimeraX

Session 2

Fee: Rs 18800

Sidechains, Rotamers & Steric Clashes

Sidechain geometry and rotamer preferences

rotamer libraries outlier sidechains environment-dependence

Steric clashes and packing defects

clashscore and bump analysis van der Waals overlaps core vs surface packing issues

Hydrogen bond and salt-bridge networks

donor/acceptor geometry electrostatic contacts water-mediated interactions

Session 3

Fee: Rs 22800

Energetics, Force Fields & Stability Checks

Energy functions and scoring terms

bonded vs non-bonded terms electrostatics / van der Waals implicit solvent models

Force-field based structure checks

AMBER / CHARMM / OPLS restrained minimization strain and hotspot identification

Stability and suitability for MD/docking

energy profiles and outliers interface vs core stability screening models before simulation

Session 4

Fee: Rs 25800

Integrated Validation Workflow & Reporting

Designing a structure validation checklist

backbone & sidechain geometry clashes & packing energy and stability metrics

Automation and batch validation

command-line validation tools Python / shell scripting integration with modelling pipelines

Deliverables: validation dossier & simulation-ready structure

clean PDB with annotations validation report (PDF/HTML) before/after comparison figures

PDF

Structure Validation Ramachandran Geometry & Energetics Training | QC, Energetics & Simulation-Ready Models

Structure Validation — Ramachandran, Geometry & Energetics — Hands-on