Structure Validation, Quality Assessment & Metrics — Hands-on

Develop a rigorous, cross platform mindset for validating macromolecular structures from X-ray crystallography, cryo-EM and NMR. This module covers geometry and stereochemistry checks, Ramachandran and rotamer outliers, clashes, map–model agreement metrics and use of wwPDB validation tools so you can deliver deposition ready, decision grade structures.

Structure Validation, Quality Assessment & Metrics

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Session Index

Session 1 — Principles of Structural Model Validation Session 2 — X-ray & Cryo-EM Fit and Global Metrics Session 3 — Geometry, Ramachandran, Rotamers & Clashes Session 4 — Validation Reports, Deposition & Case Study

Session 1

Fee: Rs 8800

Principles of Structural Model Validation

Why validation matters for structural biology

error sources in structure determination model vs data vs prior knowledge risk of over interpretation

Validation across X-ray, cryo-EM and NMR

what is common, what is modality specific data quality vs model quality wwPDB validation framework overview

Key classes of validation metrics

geometry and stereochemistry fit to experimental data global scores and outlier flags

Session 2

Fee: Rs 11800

X-ray & Cryo-EM Fit and Global Metrics

X-ray refinement and data fit scores

R / R_free basics completeness and redundancy difference maps and residual features

Cryo-EM map–model agreement metrics

global and local map CC FSC curves and resolution shells EM specific scores (overview)

Reading wwPDB validation summary plots

percentile plots vs PDB reference set understanding traffic light schemes prioritising issues for repair

Session 3

Fee: Rs 14800

Geometry, Ramachandran, Rotamers & Clashes

Backbone geometry and Ramachandran analysis

allowed, generously allowed, outliers context for glycine and proline when an outlier may be justified

Side chain rotamers, clashes and covalent geometry

rotamer libraries and outliers clashscore and contact analysis bond lengths, angles and planarity

Fixing problematic regions responsibly

using refinement and restrained rebuilding balancing data fit vs ideal geometry documenting unresolved issues

Session 4

Fee: Rs 18800

Validation Reports, Deposition & Case Study

Generating and reading validation reports

wwPDB validation server outputs per residue plots and tables summaries for collaborators and reviewers

Deposition readiness and journal expectations

PDB / EMDB deposition checklists reporting refinement and validation methods supporting information and figures

End to end validation case study

from raw validation report to polished model before vs after score comparison capturing decisions in a methods notebook

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Structure Validation, Quality Assessment & Metrics Training | X-ray, Cryo-EM & NMR Models

Structure Validation, Quality Assessment & Metrics — Hands-on