How is 3D structure determined?

Comparing 3 Primary Techniques

Where do I find experimentally determined structures?

RCSB Protein Data Bank
NCBI’s Structure Database

NCBI's iCn3D

iCn3D, pronounced 'I See in 3D,' is a web-based 3D structure viewer with a variety of analysis capabilities. The web-based nature of the tool means no downloads are needed to start visualizing and learning!

Features of interest:

• Aligns structures (PDB or AlphaFold) based on structures or sequences.
• Generates sharable links, learn more here
• Supports command-line analysis with either Python scripts, learn more here, or Node.js scripts, learn more here
• Compatible with Jupyter Notebook, learn more here
• 3D printing, learn more here
• Contact map, learn more here
• Precalculated symmetry, learn more here
• Symmetry dynamically, learn more here
• Electron density map, learn more here
• EM map, learn more here
• Transmembrane protein, learn more here
• Solvent Accessible Area, learn more here

3D Viewer Feature Comparison:

1. Aligns structures (PDB or AlphaFold) based on structures or sequences.
2. Generates sharable links could be a short URL or a URL containing the address of an iCn3D PNG Image
3. Supports command-line analysis with either Python scripts or Node.js scripts
4. Can be used in Jupyter Notebook
   
   

Shortcuts and Help Docs: