Structural Bioinformatics Foundations and File Formats — Hands-on

Build a solid foundation in structural bioinformatics by understanding how biomolecular structures are represented, validated, visualized, and prepared for downstream modeling and simulation. This module focuses on PDB and mmCIF formats, annotations, quality metrics, and practical workflows for cleaning and documenting structures.

Structural Bioinformatics Foundations and File Formats

Help Desk · WhatsApp

Session Index

Session 1 — Structural Biology Basics & Repositories Session 2 — PDB, mmCIF & Coordinate File Formats Session 3 — Visualization, Annotation & Validation Session 4 — Mini Capstone: End-to-End Structure QC

Session 1

Fee: Rs 8800

Structural Biology Basics & Repositories

Macromolecular structure levels and experimental methods

primary / secondary / tertiary / quaternary X ray crystallography NMR and Cryo EM

Coordinate systems, assemblies and symmetry

orthogonal vs fractional coordinates asymmetric unit vs biological assembly chains and symmetry operations

Structure repositories and identifiers

PDB and wwPDB partners RCSB, PDBe and PDBj AlphaFold DB overview

Session 2

Fee: Rs 11800

PDB, mmCIF & Coordinate File Formats

PDB format records and annotations

TITLE, HEADER, REMARK records ATOM / HETATM blocks TER, CONECT and MODEL

mmCIF data items and dictionaries

categories and loops atom site and entity tables metadata and validation flags

Related formats and topology information

MMTF and binary formats MOL2 and SDF for ligands topology and parameter files

Session 3

Fee: Rs 14800

Visualization, Annotation & Validation

Structure visualization and basic analysis

cartoon, surface and stick views chains, ligands, waters and ions distance and angle measurements

Mapping sequences and annotations on structures

UniProt and domain annotations active sites and motifs ligand and cofactor binding

Structure validation and basic fixing

Ramachandran and rotamer outliers clashes and geometry checks missing atoms and alternate locations

Session 4

Fee: Rs 18800

Mini Capstone: End-to-End Structure QC

Select, inspect and annotate a target structure

Theory + Practical

Clean and prepare coordinate files for modeling

resolve missing residues and atoms standardize residue and atom names generate final PDB and mmCIF

Deliverables: cleaned structure set and QC report

PDB and mmCIF files validation summary and images methodology and notes in PDF or HTML

PDF

Structural Bioinformatics Foundations and File Formats Training | PDB, mmCIF, Validation & Visualization

Structural Bioinformatics Foundations and File Formats — Hands-on