POTENTIAL PROJECTS

Theme 1. ANALYSIS OF LARGE DATASETS

1.1 Align AlphaFold and PDB Structures using VAST and Foldseek; Analysis of multiple structures for automatic capture of conformational changes (Tom, David)

1.2 Standardization of Ig datasets using a universal numbering system and CDD domains (Caesar, Jiyao, James)

1.3 Use Python or Node.js scripts to output any protein residue annotations (such as SNP, domain, binding site, secondary structure, surface area, etc) in iCn3D (Jiyao)

Theme 2. ANALYSIS OF BIOMOLECULAR INTERACTIONS AND MUTATIONS

2.1 iCn3D shows differential analysis of residue interactions of a SNP based on side chain prediction with the program scap. Backbone minimization and implicit solvent MD simulation after the side chain prediction could improve the mutation analysis. (Ravi, David, Jiyao)

2.2 Retrieve SNPs from genomics data and show them in iCn3D (Michael Sierk)

Theme 3. BIOMOLECULAR REPRESENTATIONS AND VISUALIZATION

3.1 Automatically generate 2D maps for Ig Domains and RBDs. This will be a continued effort from ISMB2021 codeathon: https://github.com/hackathonismb/2D-Maps-for-Ig-domains-and-for-RBDs (Philippe?)

3.2 Export 3D Symmetry calculated from CESymm; then import the residue mapping into iCn3D for visualization (?)

Theme 4. USER INTERFACES AND DATA SHARING MECHANISMS

4.1 Design simple iCn3D UI for middle/high school students (Sandra/Todd)

4.2 Extend iCn3D UI in React (Daniel Esposito)