Protein Structure Formats, Annotation & Quality — Hands-on

Gain practical command over protein structure file formats, annotations and quality assessment. Learn how PDB/mmCIF store coordinates and metadata, how to interpret biological assemblies and ligands, and how to use validation reports, geometry checks and refinement tools to curate reliable, publication ready structures for modeling, docking and simulation work.

Protein Structure Formats Annotation & Quality

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Session Index

Session 1 — Coordinate Formats & PDB/mmCIF Basics Session 2 — Annotation, Metadata & Biological Units Session 3 — Structure Quality Metrics & Validation Session 4 — Cleanup, Refinement & Publication Readiness

Session 1

Fee: Rs 12320

Coordinate Formats & PDB/mmCIF Basics

PDB, mmCIF and related formats

PDB legacy format limitations mmCIF data model overview BCIF and compressed archives

Coordinate records and topology

atoms, residues, chains alternate locations and occupancy hetero atoms and ligands

Visualizing and inspecting structures

PyMOL basics UCSF Chimera or ChimeraX PDBe and RCSB viewers

Session 2

Fee: Rs 16520

Annotation, Metadata & Biological Units

Metadata in PDB and mmCIF files

resolution and refinement info experimental method tags entity and chain level annotations

Biological assemblies and symmetry

asymmetric unit vs biological unit symmetry operators quaternary structure interpretation

Ligands, cofactors and sequence mapping

link records and connectivity SEQRES vs ATOM sequence missing segments and unresolved loops

Session 3

Fee: Rs 20720

Structure Quality Metrics & Validation

Geometry and stereochemistry checks

Ramachandran plots bond lengths and angles clashes and rotamer outliers

Validation reports and quality scores

PDB validation server outputs R factors and map correlation ideas global vs local quality metrics

Model to data agreement basics

electron density map inspection B factors and disorder identifying problematic regions

Session 4

Fee: Rs 26320

Cleanup, Refinement & Publication Readiness

Practical structure cleanup steps

removing waters and ions when needed adding hydrogens for modeling renumbering and chain relabeling

Local remodeling and refinement overview

side chain remodeling loop rebuilding concepts energy minimization ideas

Deliverables for modeling and manuscripts

clean coordinate sets for docking or MD figure ready views validation summaries for reviewers

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Protein Structure Formats, Annotation & Quality Training | PDB/mmCIF, Validation & Curation

Protein Structure Formats, Annotation & Quality — Hands-on