PDB-101: Learn: Guide to Understanding PDB Data: Introduction
Training and outreach portal of
Molecular explorations
through biology and medicine
Training and outreach portal of
Guide to Understanding PDB Data
Introduction
PDB Overview
Protein Hierarchical Structure
Beginner’s Guide to PDBx/mmCIF
Missing Coordinates and Biological Assemblies
Dealing with Coordinates
Primary Sequences
Biological Assemblies
Computed Structure Models
Small Molecule Ligands
Exploring Carbohydrates
Methods for Determining Structure
Crystallographic Data
Molecular Graphics Programs
Introduction to RCSB PDB APIs
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 with
Introduction 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 in
Beginner’s Guide to PDBx/mmCIF Format
The details of atomic coordinates are described in
Dealing with Coordinates
If you want to download many PDB files and/or PDB data, look at
Introduction 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 with
Missing Coordinates
Ensuring that you’re exploring the functional
Biological Assembly
of your biomolecule
Exploring the relationship of the
Primary Sequence
and the 3D structure
If you have questions about the biology of biomolecules and how it is expressed in PDB structures, explore:
Hierarchical Structure of Proteins
Exploring Carbohydrates
Small Molecule Ligands
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 in
Methods for Determining Structure
A more detailed description of X-ray crystallography is included in
Crystallographic Electron Density, Resolution, and R-value
Computation methods are presented in
Computed 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.
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RCSB PDB Core Operations are funded by the
U.S. National Science Foundation
(DBI-2321666), the
US Department of Energy
(DE-SC0019749), and the
National Cancer Institute
National Institute of Allergy and Infectious Diseases
, and
National Institute of General Medical Sciences
of the
National Institutes of Health
under grant R01GM157729.