PHGDH Project Dashboard
Auto-regenerated by project_dashboard.py at 2026-05-04 17:05:00. Cells are color-coded by Achievement score (1-9 reverse-NIH, 9 best): green ≥5 yellow 4 red ≤3
Table 1 — PLEASER × Iterations (AGE scores)
Each cell shows an AGE triple (Achievement.Growth.Efforts) on the reverse-NIH scale (9=best). Click to open the source report.
No closed PLEASER iterations yet. Iteration 1 (Task 2.1) in stage P (Plan). Table will populate after the first L3 report.
PLEASER Iteration ledger
See iterations.md for the full per-task per-iteration record (Problem / Methods / Findings / Conclusion / Outstanding / AGE / Expense per stage).
Updated automatically when each iteration closes (data provenance gate in post_r_watchdog.py).
Table 2 — Aims / Tasks — progress & Achievement
Achievement = reverse-NIH 1-9 (9 best, 5 satisfactory). Tasks may run in parallel, locally on W0/L0 or remotely on Cheaha.
| Work item | Status | % complete | Achievement |
|---|---|---|---|
| Aim 1 — Automated data pipeline | — | — | — |
Task 1.1 — Daily ChEMBL scavenge + delta reporting | ✓ done | 100% | 7 |
Task 1.2 — Scaveng→Hermes enrichment loop (rank new molecules, seed wiki pages) | ○ pending | — | — |
Task 1.2.a — Implement ranker script for ChEMBL delta parsing | ○ pending | — | — |
Task 1.2.b — Automated wiki stub creation for top hits | ○ pending | — | — |
Task 1.3 — Entity-page templates (molecule / target / pathway / gene-set) | ○ pending | — | — |
Task 1.3.a — Molecule template design (SMILES, properties) | ○ pending | — | — |
Task 1.3.b — Target/Pathway template design (UniProt, KEGG) | ○ pending | — | — |
| Aim 2 — Computational analysis of PHGDH inhibitors | — | — | — |
Task 2.1 — pChEMBL distribution figure | ✓ done | 100% | 7 |
Task 2.2 — Top-20 PHGDH inhibitors by pChEMBL ≥ 7 | ✓ done | 100% | 7 |
Task 2.3 — PDB binding-site annotation (4NJN/6RIH/7S3R + more) | ✓ done | 100% | 7 |
Task 2.4 — Scaffold clustering of top-20 (RDKit Murcko) | ○ pending | — | — |
| Aim 3 — Literature synthesis & knowledge graph | — | — | — |
Task 3.1 — PubMed sweep “PHGDH all allosteric / RBD” 2024-2026 | ✓ done | 100% | 7 |
Task 3.2 — Wiki page phgdh-scavenger — pipeline, schema, output | ○ pending | — | — |
Task 3.2.a — Document technical pipeline & data schema | ○ pending | — | — |
Task 3.2.b — Create “How-to” guide for scaffold scavenger | ○ pending | — | — |
Task 3.3 — Monthly 2025 AI-drug-discovery digest (Jan 2025) | ○ pending | — | — |
Task 3.3.a — ArXiv curation (Jan 2025) | ○ pending | — | — |
Task 3.3.b — Generate summary for Telegram/Wiki | ○ pending | — | — |
Task 3.4 — Publish 3 wiki drafts + 20 Gemma concept stubs | ○ pending | — | — |
Task 3.4.a — Metadata & link audit for new pages | ○ pending | — | — |
Task 3.4.b — Git automation (commit/push) for all drafts | ○ pending | — | — |
| Aim 4 — Structure-based virtual screening on Cheaha HPC | — | — | — |
Task 4.1 — Cheaha workspace setup + first dock | ✓ done | 100% | 7 |
Task 4.2.a — Filter hits by docking score | ○ pending | — | — |
Task 4.2.b — Cluster hits by scaffold | ○ pending | — | — |
Task 4.2.c — Re-score top-50 with short MD | ○ pending | — | — |
Task 4.2.d — Generate Scatter plot (Score vs. Ligand Efficiency) | ○ pending | — | — |
Task 4.2.e — Export ranked results to CSV | ○ pending | — | — |
Task 4.3 — Scale-out: top-500 SMILES virtual screen | ○ pending | — | — |
Task 4.4 — Port Fan Li 2026 CLM: LSTM pretrain + 5-step incremental FT on PHGDH SMILES | ▶ ACTIVE | 30% | 5 |
Task 4.5 — Vina rerank top-500 CLM generations into 6RIH K4T pocket | ○ pending | — | — |
Task 4.6 — Bimodal combined-score shortlist + synthesis triage | ○ pending | — | — |
| Aim 5 — Scientific deliverables | — | — | — |
Task 5.1 — Paper introduction draft | ○ pending | — | — |
Task 5.2 — Repo README + pipeline diagram | ○ pending | — | — |
Task 5.3 — Poster (L4 deliverable) | ○ pending | — | — |
Pending publish
- Total project pages on W0: 101
- New (not yet on sdd-wiki): 15
- Changed since last publish: 6
Pressing Publish to sdd-wiki on the dashboard will push these:
| File | Status | SHA diff |
|---|---|---|
PHGDH-Allosteric-RBD-Binder/Project-Dashboard.md | CHANGED | e25e89e9de547fc2→eedb4d3f2a68b131 |
PHGDH-Allosteric-RBD-Binder/Project-Summary.md | CHANGED | 5d2a6daadeb557e8→b86add72195bfd61 |
PHGDH-Allosteric-RBD-Binder/iter-3/iter-3-report.md | NEW | — |
PHGDH-Allosteric-RBD-Binder/methods/MD-Simulation-Setup.md | NEW | — |
PHGDH-Allosteric-RBD-Binder/paper_results/README.md | NEW | — |
PHGDH-Allosteric-RBD-Binder/paper_results/corpus-stats/README.md | NEW | — |
PHGDH-Allosteric-RBD-Binder/paper_results/iter-5-rl/iter-5-report.md | NEW | — |
PHGDH-Allosteric-RBD-Binder/paper_results/methods/methods.md | NEW | — |
PHGDH-Allosteric-RBD-Binder/paper_results/next-steps.md | NEW | — |
PHGDH-Allosteric-RBD-Binder/reports/L1/2026-05-01.md | CHANGED | 3b630a29652e12b9→9553b277a80ca9ee |
PHGDH-Allosteric-RBD-Binder/reports/L1/2026-05-02.md | NEW | — |
PHGDH-Allosteric-RBD-Binder/reports/L1/2026-05-03.md | NEW | — |
PHGDH-Allosteric-RBD-Binder/reports/L1/2026-05-04.md | NEW | — |
PHGDH-Allosteric-RBD-Binder/reports/L2/2026-05-01.md | CHANGED | b4de77e705768df4→7f5f9620c63d9a2c |
PHGDH-Allosteric-RBD-Binder/reports/L2/2026-05-02.md | NEW | — |
| … and 6 more |
Summary
- Tasks total: 34
- Done: 6 · Active: Task 4.4 · Pending: 27
- PLEASER iterations closed: 0
Every cell link points at a source report verified at dashboard generation time (2026-05-04 17:05:00). If a link 404s, the report was moved or deleted since last generation; re-run the dashboard.
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