New Features in iCn3D: Expanded Analysis of AlphaFold Structures, Virtual & Augmented Reality

New Features in iCn3D: Expanded Analysis of AlphaFold Structures, Virtual & Augmented Reality

We have added several exciting features to our interactive, web-based 3D-structure viewer, iCn3D! These new features allow you to compare AlphaFold Predicted structures to available structures as well as experience 3D structures with virtual and augmented reality. Learn more about tool updates here.

AlphaFold is an artificial intelligence system designed to compute protein 3D structure from protein sequence information. A large corpus of such predicted structures is available from the UniProt resource. This data can be loaded into and visualized with the iCn3D structure viewer. iCn3D provides rich annotations of 3D structures, including conserved domain footprints, compact structural sub-domains, functional sites, and sequence variation. Figure 1 shows an example of one of the AlphaFold predictions loaded in iCn3D.

Figure 1. iCn3D display of annotations (domains, SNPs, ClinVars, etc.) of AlphaFold structure (UniProt ID Q08426).

Comparing AlphaFold and PDB Structures

To find experimentally determined 3D structures that are similar to a predicted coordinate set, use “NCBI VAST(PDB)” in the iCn3D menu (“File > Search Similar”). Once you have identified similar structures, you can then align your query structure with a selected neighbor (“File > Align > Multiple Chains”). Here, you have three options to choose from: 1) align these structures by structure alignment, either by VAST or TM-align, 2) align these structures by sequence alignment first, followed by a superposition of the mapped residue coordinates, or 3) align the structures based on the predefined, mapped residues. Figure 2 shows a multiple alignment produced by structure alignment with VAST in iCn3D.

Figure 2. Multiple alignment in iCn3D of AlphaFold and PDB structures (UniProt IDs P69905 and P01942, and PDB ID 1HHO).

If you are working with a local PDB file, you can load selected neighbors in iCn3D using the menu (“File > Retrieve by ID > MMDB or AlphaFold IDs”), then load your PDB file through the menu (“File > Open File > PDB Files (appendable)”), and finally realign these structures through the menu (“File > Realign Selection”).  As with the multiple chain alignment example described above, you have three options: 1) “by Structure Alignment”, 2) “by Sequence Alignment”, and 3) “Residue by Residue”, which uses the predefined residue mapping.

VR & AR views

With the release of iCn3D version 3.12, you can view 3D structures in a Virtual Reality (VR) setting (Figure 3) with a VR headset, and in an Augmented Reality (AR) setting with Google Chrome browser in an Android phone.

For a VR headset, you should open a browser in your headset, view a 3D structure in iCn3D and then click the button “ENTER VR” located at the bottom of the browser window. You can use the right trigger to move forward and use the left trigger to move backward.

To use AR on an Android phone, open an iCn3D view in Chrome. Then click the button “START AR” to see the 3D structure embedded in your surroundings. You can tap once on the screen to locate a minimized 3D structure in your tapped location and tap twice quickly to scale up the 3D structure.

Figure 3. VR view of 3D structures in iCn3D.

If you have any questions or feedback for the iCn3D team, please write to the help desk.

Leave a Reply