NCBI tutorial: iCn3D hands-on workshop
“I see in 3D” (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode […] – (Longer description.)
This workshop is designed for life scientists with some (intermediate) expertise in structural biology. The topics of structure prediction, molecular docking, or molecular dynamics simulations will not be explored.
Presented by NCBI Faculty Alexa Salsbury, PhD
Materials:
– Workshop pages (HTML)
– Slides (PDF)
– Video Recording: Exploring 3D Molecular Structures with iCn3D
Topics covered:
– Where to find information on motifs, domains, and similar structures
– How to analyze 3D structure and highlight important features like active site residues, point mutations, and binding partners
– How to compare AlphaFold and PDB Files
– How to save and share visualization files
Comparison table
This comparis0n table appears within the slides PDF and can be a useful to decide interest. Software links have been added.
| Web- based | 1D Sequence | 2D Diagram | Annotation | Align | Share Link | Script | Jupyter Notebook | Virtual Reality | 3D Printing |
|---|---|---|---|---|---|---|---|---|---|
| iCn3D | ✓ | ✓ | ✓ | ✓ | ✓a | ✓b | ✓c | ✓d | ✓ |
| Mol* | ✓ | ✓ | Web | Web | |||||
| Aquaria | ✓ | ✓ | ✓ | ✓ | |||||
| Chimera | ✓ | ✓ | ✓ | ||||||
| PyMol | ✓ | ✓ | ✓ | ||||||
| Cn3D | ✓ | Web | ✓ | ✓ |
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.
(Note: Chimera is legacy software that is no longer being developed or supported. Users are strongly encouraged to try UCSF ChimeraX, which is under active development.)