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", Structure Viewer is a web-based 3D viewer with structure analysis capabilities. The web-based nature of the tool means no downloads are needed to start visualizing and learning!

iCn3D features of interest:

• iCn3D aligns structures (PDB or AlphaFold) based on structures or sequences.
• iCn3D sharable links (https://structure.ncbi.nlm.nih.gov/icn3d/share.html?XCxR6fSTmXHxR3o1A)
• iCn3D supports command-line analysis with either Python scripts (https://github.com/ncbi/icn3d/tree/master/icn3dpython) or Node.js scripts (https://github.com/ncbi/icn3d/tree/master/icn3dnode)
• iCn3D can also be used in Jupyter Notebook (https://pypi.org/project/icn3dpy)
• 3D printing:  structure.ncbi.nlm.nih.gov/icn3d/share.html?wt4TDqzhC2rhCYTD7
• Contact map: structure.ncbi.nlm.nih.gov/icn3d/share.html?rnMbe26tNsAjJLGK9
• Precalculated symmetry: structure.ncbi.nlm.nih.gov/icn3d/share.html?bGH1BfLsiGFhhTDn8
• Symmetry dynamically: structure.ncbi.nlm.nih.gov/icn3d/share.html?6NvhQ45XrnbuXyGe6
• Electron density map: structure.ncbi.nlm.nih.gov/icn3d/share.html?QpqNZ3k65ToYFvUB6
• EM map:  structure.ncbi.nlm.nih.gov/icn3d/share.html?L4C4WYE85tYRiFeK7
• Transmembrane protein: structure.ncbi.nlm.nih.gov/icn3d/share.html?jMN16mJyR9STUx6E6
• Solvent Accessible Area: structure.ncbi.nlm.nih.gov/icn3d/share.html?xKSyfd1umbKstGh29

3D Viewer Feature Comparison:

a: iCn3D aligns structures (PDB or AlphaFold) based on structures or sequences.

b: iCn3D sharable links could be a short URL or a URL containing the address of an iCn3D PNG Image

c: iCn3D supports command-line analysis with either Python scripts or Node.js scripts

d: iCn3D can also be used in Jupyter Notebook

iCn3D Shortcuts and Help Docs:

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