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PDB and Data Archiving Curriculum

Use PDB data to their full extent: Understanding PDBx/mmCIF

Virtual Crash Course | May 3, 2023

Understand the basics of PDBx/mmCIF data dictionary and file format that underpin archiving of more than 200,000 experimentally determined three-dimensional biostructures in the PDB. Learn about software tools for generating and working with PDBx/mmCIF files, and programmatic access for harvesting PDB data.

After watching the videos featured in this course, you will be able to:

  • Understand PDBx/mmCIF format as data model
  • Know software tools for generating, editing, and visualizing PDBx/mmCIF files
  • Understand PDBx/mmCIF dictionary extensions, including ModelCIF for computed structure models (CSM) from AI/ML
  • Parse data from PDBx/mmCIF files for your research

Additional materials for this course are available:

Click on the image below to play the video.

Introduction

Stephen K. Burley

Director, RCSB Protein Data Bank

Introduction and course objectives

Gregg Crichlow

Biocurator, RCSB PDB, Rutgers University

PDBx/mmCIF format - Not your parents’ legacy PDB format

Ezra Peisach

Scientific Software Developer/PDBx mmCIF Dictionary Manager, RCSB PDB, Rutgers University

PDBx/mmCIF data files - Lifting the lid off the black box

Brian Hudson

Biocurator, RCSB PDB, Rutgers University

Programmatic data access and analysis using PDBx/mmCIF files, Part 1

Irina Persikova

Biocuration Lead Deputy, RCSB PDB, Rutgers University

Programmatic data access and analysis using PDBx/mmCIF files, Part 2

Chenghua Shao

Scientific Software Developer/KPI Evaluator, RCSB PDB, Rutgers University