Introduction
Guide to Understanding PDB Data is designed to help you get started with finding and exploring the hundreds of thousands of 3D structures in the PDB archive.
If you’re new to the world of structural biology, start withIntroduction to the PDB.
If you have questions about PDB data, several pages will help:
- The logic for how structures are annotated, classified, and stored is presented inBeginner’s Guide to PDBx/mmCIF Format
- The details of atomic coordinates are described inDealing with Coordinates
- If you want to download many PDB files and/or PDB data, look atIntroduction to RCSB PDB APIs
Biological molecules are complicated and diverse, and experimental techniques aren’t always perfect, so several pages describe challenges you’ll face when exploring PDB files. These include:
- Dealing with structure files withMissing Coordinates
- Ensuring that you’re exploring the functionalBiological Assembly of your biomolecule
- Exploring the relationship of thePrimary Sequence and the 3D structure
If you have questions about the biology of biomolecules and how it is expressed in PDB structures, explore:
Molecular Graphics Programs offers an introduction to different ways to display biomolecules.
Many experimental and computational techniques are used to determine the structures of biomolecules.
- Experimental methods are presented inMethods for Determining Structure
- A more detailed description of X-ray crystallography is included inCrystallographic Electron Density, Resolution, and R-value
- Computation methods are presented inComputed Structure Models
Except where noted, this feature is written and illustrated by David S. Goodsell.
About PDB-101
Researchers around the globe make 3D structures freely available from the Protein Data Bank (PDB) archive. PDB-101 training materials help graduate students, postdoctoral scholars, and researchers use PDB data and RCSB PDB tools. Outreach content demonstrate how PDB data impact fundamental biology, biomedicine, bioengineering/biotechnology, and energy sciences in 3D by a multidisciplinary user community. Education Materials provide lessons and activities for teaching and learning.
PDB-101 is developed by theRCSB PDB.
RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.