PDB Structures — Quality Metrics & Remediation — Hands-on

Learn how to read, assess, and remediate macromolecular structures from the PDB so that they are fit for downstream docking, simulation and design workflows. You will work end-to-end from raw PDB/mmCIF inspection to validation, repair, and deposition-ready curated models.

PDB Structures — Quality Metrics & Remediation

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Session Index

Session 1 — PDB/mmCIF Formats & Structure Anatomy Session 2 — Quality Metrics & Validation Dashboards Session 3 — Structure Remediation & Optimization Session 4 — Deposition-Ready Models & Case Study

Session 1

Fee: Rs 11800

PDB/mmCIF Formats & Structure Anatomy

PDB/mmCIF basics and coordinate models

RCSB / PDBe / PDBj AlphaFold DB links biological vs asymmetric unit

Structure anatomy and annotations

chains / residues / ligands altLoc / occupancy waters / ions / cofactors

Toolchain for inspection

PyMOL UCSF ChimeraX pdb-tools / Biopython

Session 2

Fee: Rs 15800

Quality Metrics & Validation Dashboards

Geometric quality checks

bond lengths / angles Ramachandran & rotamers chiral centers & planarity

Global and local validation statistics

R / R_free B-factor profiles clashscore / MolProbity

Density & map-based validation (X-ray / cryo-EM)

RSCC / RSR FSC curves validation reports & dashboards

Session 3

Fee: Rs 19800

Structure Remediation & Optimization

Fixing common structural issues

missing sidechains / loops altLoc clean-up chain IDs & residue numbering

Protonation, hydrogens & local refinement

hydrogen placement pK_a-aware protonation H-bond & salt-bridge networks

Automated re-refinement workflows

pdb-redo Phenix / REFMAC before–after metric comparison

Session 4

Fee: Rs 22800

Deposition-Ready Models & Case Study

Preparing curated structures for downstream use

docking-ready clean PDB biological assemblies ligand & cofactor handling

Building a QC & remediation checklist

standard operating steps automation via scripts integration with MD / docking pipelines

Deliverables: curated model & validation dossier

clean PDB/mmCIF validation report (PDF/HTML) before/after comparison slides

PDF

PDB Structures Quality Metrics & Remediation Training | Validation, Repair & Deposition-Ready Models

PDB Structures — Quality Metrics & Remediation — Hands-on