zorgster
commented
1 year ago It would be really useful if there was a function in the viewer toolbox that allowed one to, say, drop a custom list of RVs or vcf format into an input box and have them highlighted on the model to see if they group in the same region of the protein. And shaded for AF (with the ability to dynamically switch between different populations). That may be a feature request rather than a mol viewer suggestion, but Ensembl do that with Mol* in a limited way.
Ensembl use Mol (https://molstar.org) for both PDBs and Alphafold. The models are attached to transcripts of the gene. On their UI, you can highlight all amino acids from SIFT (or Polyphen) variants and switch those on and off individually. Not all variants show up and I can't add a custom list. But demonstrates that Mol can do the above. It is also accessible via VEP, but I haven't explored whether that only shows one variant or all variants in your analysis.
There is also KNIME MolViewer - https://github.com/3D-e-Chem/molviewer-tsx
mattsolo1
My favorite instance of the Mol* viewer is the one on the PDB website. See example: https://www.rcsb.org/3d-sequence/1NQ2
I think we may want a similar design as this.
Some docs: https://www.rcsb.org/docs/sequence-viewers/3d-protein-feature-view
And source code for their viewer: https://github.com/rcsb/rcsb-saguaro-3d
There is also a 1D viewer component, but perhaps we can use our own plotting libraries instead to stay consistent with the rest of the site.