Protein Structure Databases & Visualization Tools — Hands-on

Learn to find, evaluate, and visualize macromolecular structures with modern databases and viewers. Build clean, reproducible figure pipelines and validation reports ready for manuscripts.

Protein Structure Databases & Visualization Tools

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Session Index

Session 1 — Structure Databases & Formats Session 2 — Viewers & Publication Figures Session 3 — Validation & Quality Checks Session 4 — Mini Capstone: Structure Report

Session 1

Fee: Rs 6300

Structure Databases & Formats

Core resources, accessioning, and identifier mappings

RCSB PDB PDBe AlphaFold DB EMDB UniProt

File formats, annotations, and crosswalks

PDB/mmCIF PDBx SIFTS FASTA

Download automation & metadata filtering

APIs CLI programmatic queries

Session 2

Fee: Rs 8400

Viewers & Publication-Quality Figures

Interactive exploration and scene management

PyMOL UCSF ChimeraX VMD Mol* NGL

Representations, coloring, and annotations

cartoons surfaces ligand highlighting ray tracing

Reproducible figure pipelines & exports

sessions/scripts SVG/PNG panels

Session 3

Fee: Rs 11200

Validation & Quality Assessment

Geometry checks and statistics for reliability

Ramachandran rotamers clashscore B-factors

Tools & map fit for X-ray/cryo-EM models

MolProbity EMRinger Q-score

Best practices: provenance and reproducibility

checklists versioning

Session 4

Fee: Rs 14000

Mini Capstone: Structure Report

Assemble a complete structure dossier for a target

Theory + Practical

Scenes, figure panels, and validation summary

PyMOL/ChimeraX scripts Mol* snapshots report templates

Deliverables: figures, tables, README & manifest

PDF CSV/TSV checksums

PDF

Protein Structure Databases & Visualization Tools Training | PDB/PDBe, AlphaFold DB, PyMOL/ChimeraX/VMD, Validation

Protein Structure Databases & Visualization Tools — Hands-on