# Stage 2 Controlled Public-Alpha Status

## Current status

Stage 2 MD Evidence is now a controlled public-alpha live MD worker MVP.

It has passed:

- Spaces upload foundation
- object verification
- Stage 2 worker download/hash/artifact package
- public AdK single-job MD parsing gate
- public AdK 5-job MD parsing gate
- public AdK 10-job MD parsing gate
- researcher-style uploaded small trajectory gate
- PDB + DCD format compatibility gate
- GRO + XTC format compatibility gate
- medium researcher-style uploaded trajectory gate

## What Stage 2 can currently do

Stage 2 can:

- accept topology, trajectory, and metadata files through the website
- upload files directly from browser to DigitalOcean Spaces
- verify uploaded objects
- create a persistent Stage 2 worker job
- download uploaded files from Spaces
- compute file SHA-256 hashes
- parse compatible topology/trajectory pairs with MDAnalysis
- extract frame count, atom count, residue count
- compute descriptive RMSD, RMSF, and radius-of-gyration summaries
- write JSON, CSV, Markdown, manifest, and SHA-256 artifacts
- display a persistent result page

## What Stage 2 cannot claim yet

Do not claim:

- protein-stability prediction
- biological mechanism proof
- binding prediction
- inhibitor analysis
- therapeutic advice
- clinical guidance
- pharma-grade decision support
- arbitrary trajectory compatibility
- large-file production reliability
- high-volume multi-user service

## Recommended pilot usage

Use Stage 2 for controlled small-trajectory pilots only.

Recommended first researcher-pilot profile:

- one topology file
- one trajectory file
- one metadata file
- small-to-moderate trajectory
- parseable by MDAnalysis
- access-code gated upload
- descriptive metrics only

## Next engineering gates

1. Format compatibility matrix.
2. One real external researcher small trajectory.
3. 10 researcher-style small uploads.
4. Larger-file multipart upload.
5. Queue, quotas, monitoring, and retention policy.