AlphaFold Stoichiometry Generator

A Shiny app for generating AlphaFold multimer input files with systematic stoichiometry exploration.

What It Does

• Input protein sequences via paste or FASTA upload (any number of proteins)
• Set stoichiometry ranges per protein (min/max copy numbers)
• Generate combinations — all combos, random subsets, or homomer series
• Preview AlphaFold3 JSON, multimer FASTA, and text summaries
• Download individual models or bulk ZIP with manifest

Install & Run

# Install dependencies (one time)
install.packages(c("shiny", "DT", "jsonlite", "zip"))

# Run the app
shiny::runApp("App.R")

No Bioconductor dependencies. No external APIs. Four CRAN packages. Works offline.

Usage

1. Paste or upload your protein sequences in FASTA format
2. Click Parse to load them
3. Set min/max copy numbers for each protein in the sidebar
4. Choose generation mode:
   • All combinations — full cartesian product of copy number ranges
   • Random subset — sample N random stoichiometries
   • Quick homomer series — each protein independently (monomer → multimer)
5. Click Generate Models
6. Preview any model's JSON/FASTA in the Preview tab
7. Download from the Download tab

Output Formats

AlphaFold3 JSON

Ready to paste into the AlphaFold3 server. Uses the proteinChain format with count field.

Multimer FASTA

Each chain as a separate entry (e.g., >ProteinA_copy1, >ProteinA_copy2).

Manifest CSV

Tracks all generated models with chain counts, residue totals, and warnings.

Residue Limit Warning

Models exceeding 3,000 total residues are flagged — AlphaFold performance degrades significantly above this threshold.

License

Released under the GNU General Public License v3.0. See LICENSE for details.