GeoDock

5-30 minutesPaperCodeProduction Ready

Deep learning protein-protein docking with SE(3) equivariance

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_ready_api_slurm_graylab_geodock_cpu
Storage: 5-20
Strategy: compiled/binary SIF or shared python312_slim + ext3 overlay
Next: Production Ready. Optional hardening: expose user partner-PDB upload controls, GPU acceleration, and optional OpenMM refinement.

SOP probe used fallback public source https://github.com/Graylab/GeoDock revision df8d1f4c24ae2946655f27e7411ba2ffabf3d350 because requested drorlab/geodock was not cloneable from server. Installed at /media/nik/seagate_nik/bio_server/tools/geodock using shared python39 SIF plus pip --target deps. Source 130M, deps 7.7G, ESM cache 2.5G. CPU Slurm job 320 produced sane docked PDB: 100288 bytes, 1474 atoms, 300 CA atoms, chains A/B, 0 bad coordinates. First-run runtime 1934s mostly ESM download/cache; dock call about 30s. GPU path not validated. 2026-07-08T21:13:50+08:00: Production Ready promotion: backend runner API job 9e600e5318f9 / Slurm job 570 completed through the web runner API using Graylab/GeoDock revision df8d1f4c24ae2946655f27e7411ba2ffabf3d350, python39.sif, cached ESM2 model, and checkpoint dips_0.3.ckpt. External recheck found Graylab/GeoDock and PyPI geodock identify Graylab as the public official GeoDock repository/package; the catalog drorlab/geodock link was stale/not cloneable. Produced zero-byte slurm.out/slurm.err and empty geodock_stderr.txt; geodock_docked.pdb was 100288 bytes with 1474 atom records and chains A/B; runtime reported runner_init_seconds 16.1 and dock_seconds 16.419 on CPU/no-refine.