This file maps the active local protein-design objective to concrete evidence in the repo. It is a verification aid, not a claim that the system is biologically validated.
| Requirement | Evidence | Status |
|---|---|---|
| Document the full workflow end to end | README.md, protein_loop_runbook.md, protein_loop_workflow_map.md, protein_loop_architecture.md | Verified |
| Explain what each tool does and how the stages connect | protein_loop.md, outputs/protein_loop_system_map.md | Verified |
Separate MOCK / DEMO artifacts from live run outputs |
protein_loop_status.md, protein_loop_completion_checklist.md, outputs/openfold3_run_review.md | Verified |
| Standardize the local orchestration layer | outputs/protein_loop_runner.py, protein_loop.py | Verified |
| Generate backbone / design / MSA / paired-MSA / fold / summary artifacts | outputs/helical_bundle_backbone.pdb, outputs/helical_bundle_folded.pdb, outputs/openfold3_msa_mock.a3m, outputs/openfold3_paired_msa_mock.csv, outputs/protein_loop_run_summary.json |
Verified |
| Score and compare runs deterministically | outputs/openfold3_msa_weighting_pipeline.py, outputs/openfold3_run_comparison.json, outputs/openfold3_run_registry.json |
Verified |
| Update heuristic defaults from prior runs with explicit logged rules | outputs/openfold3_next_run_command.txt, outputs/openfold3_next_run_rationale.txt, outputs/openfold3_feedback_state.json |
Verified |
| Verify the live evidence chain end to end | protein_loop_verify.py, outputs/protein_loop_verification_report.json |
Verified |
| Provide a single-command bootstrap path for the loop and verifier | protein_loop_bootstrap.py, outputs/protein_loop_bootstrap_report.json |
Verified |
| Provide a combined health verdict across verification and reproducibility | protein_loop_assess.py, outputs/protein_loop_assessment_report.json |
Verified |
| Provide a current-state dashboard for operators | protein_loop_dashboard.py, protein_loop_current_state.md |
Verified |
| Keep external BioNeMo calls optional and separate from the local core | protein_loop.md, protein_loop_runbook.md, protein_loop_completion_checklist.md |
Verified |
- The system is still labeled
MOCK/DEMO. - The feedback loop is heuristic, not learned self-training.
- The repo does not yet contain a validated biological generation claim.
- External BioNeMo calls are documented but not required for the local core.