iCn3D 2.15.0 is now available on NCBI web site and as a release on GitHub. To use the updated web application, retrieve any structure from the Molecular Modeling Database (MMDB), open the structure summary page, and click the button for “full-featured 3D viewer” in the molecular graphic. For example, you can retrieve structures that contain the term SARS-COV-2, click on a structure of interest, then follow the link for “full-featured 3D viewer.” You can also open iCn3D and use the “File” menu to retrieve a structure by its ID, for example 6MOJ, or to open a structure file from your local computer. Figure 1. iCn3D showing the structure of the SARS-COV-2 spike protein (6MOJ) with custom coloring of conserved residues and a multiple sequence alignment of other coronavirus spike proteins. The ability to apply custom color to specific residues or chains and the ability to add multiple alignments as tracks are some of the new features available in 2.15.0
A gallery with live examples that now includes SARS-CoV-2-related structures such as the spike protein show in Figure 1 demonstrates a variety of ways that you can use iCn3D to view and analyze structures. The iCn3D Web APIs document describes how to use the iCn3D structure viewer in your own web page. See the MMDB news page for a more detailed list of new features available in iCn3D as well as some useful examples.