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:
- Presentation Slides
- PDBx/mmCIF Dictionary website
- Beginner’s Guide to PDB Structures and the PDBx/mmCIF Format
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
