The NCBI structure viewer iCn3D version 3 is now available on the NCBI web site and from GitHub.
Analysis of 3D Structures
You can use the current version with the icn3d package at npm to write scripts to call functions in iCn3D. For example, this script on GitHub can calculate the change in interactions due to a mutation. The results of this analysis for the structure (6M0J) of the SARS-CoV-2 spike protein bound to the ACE2 receptor are displayed in Figure 1. These show the predicted changes in interactions with other residues in the the SARS-CoV-2 spike protein and in the ACE2 receptor when the asparagine (N) at position 501 of the spike protein is changed to a tyrosine (Y). You can also run these scripts from the command line to process a list of 3D structures to get and analyze annotations.
Figure 1. iCn3D viewer showing the predicted interactions with other residues in the spike protein and in the ACE2 target when the asparagine (N) at position 501 of the SARS-CoV-2 spike protein is substituted with tyrosine (Y), highlighted in yellow. Interactions were calculated using the script interactions2.js.
The classes and functions are listed in the iCn3D documentation. To find functions, you can first generate a custom view in iCn3D interactively and use the menus to display the functions. For example (Figure 2), you can click the menu “Analysis > Mutation” to see the “Interactions” of the mutations “6M0J_E_501_Y”. Then you can click the menu “File > Share Link” to see the commands in the section “Original URL with commands”.
Figure 2. iCn3D viewer showing Mutation and Share link menus that show the interactions and commands.
Most commands are processed with functions in the file “applyCommand.js”. Other commands with asynchronized retrieval are processed in the file “loadScript.js”.
Since the JavaScript code of iCn3D was upgraded from ES5 to ES6, the embedding of iCn3D has some changes described in the help document.