Fig 1.
Starting from user-provided variant genomic coordinates (top left), VUStruct identifies missense variants and maps them onto protein structures which VUStruct automatically curates from experimental depositions and model databases.
Various parallel calculations are then launched on the HPC, as enumerated in the text.
Fig 2.
Screenshot from the VUStruct-generated case report landing web page.
In the table, each row summarizes the range of calculated values for each variant. Ranges arise in some calculations because multiple structures are considered for each transcript. In the case of input genomic coordinates, multiple transcript isoforms are often impacted for each variant. The “Refresh Cluster Jobs Information” box allows detailed monitoring and troubleshooting. The drawn red box shows how summary row 14 (a change to gene HFE on Chrom 6) has been expanded to display five rows for different impacted transcripts. The first of row corresponds to the canonical UniProt isoform. Clicking the “Report” link for that line will display detailed calculations for this variant in the context of that transcript (see next Fig).
Fig 3.
Screenshot of the VUStruct-generated transcript variant report, showing the variant location as a pink diamond in the context of the protein’s PFAM domain [53] annotation.
This is followed by results for Rate4Site, COSMIS, MusiteDeep, and ScanNet calculations. A key table is the Structure Summary, which lists all the structures (from the PDB, MODBASE, SWISS-MODEL database, and AlphaFold database) on which calculations were performed. For example, the highlighted row summarizes all the calculations performed on X-Ray crystal structure 1a6b.pdb, and the highlighted shortcut in the left column leads to the section of the page detailing those results (see next Fig).
Fig 4.
Screenshot of a section of the VUStruct results page, which foreach structural model shows the results of the ΔΔG and PathProx calculations, highlighted in red, along with associated statistics to judge reliability.
Each structure is displayed in a customized and interactive NGL Viewer [19] session. This view can be used to understand the structural context of the variant (highlighted here with a gray text pop-up. For example, one can display all pathogenic and likely pathogenic ClinVar variants (shown as red spheres), or color the model according to AlphaFold confidence or by PathProx score (from low- blue, to high - red - as shown above). Figs to illustrate a structural mechanistic hypothesis can be generated quickly from these images.