SAA computation example

Secondary structure, complex coordinates with a 122-aa reference SAA sequence, and execution records for one 38-nt DNA selection candidate.

Energy, confidence and distances are computational outputs; they do not establish experimental binding or affinity.

Fresh secondary-structure calculation

Engine: ViennaRNA 2.7.2
Parameters: Mathews 2004 · DNA
Temperature: 37 °C
MFE: -1.60 kcal/mol

.....(((......))).....................

Parameters and calculation provenance

Retained selection observations

Round	Count	Denominator	%
R1	0	151,245	0
R3	61	145,026	0.042061
R5	301	111,867	0.26907
R7	9,331	146,005	6.3909
R8	15,376	136,825	11.238
R9	11,758	117,652	9.9939

Fresh complex prediction

Boltz-2: 2.2.1
ipTM: 0.411
Mean pLDDT: 68.1 / 100
Closest cross-partner heavy atoms: 2.418 Å
Atom pairs below 2 Å: 0

Drag to rotate · scroll to zoom. Protein: teal; DNA: orange.

The distance screen does not replace complete stereochemical validation.

Computed contact pairs (≤5 Å)

DNA	Protein	Minimum heavy-atom distance
B:12	A:92	4.307 Å
B:18	A:111	4.722 Å
B:18	A:112	4.867 Å
B:19	A:109	3.279 Å
B:19	A:111	4.768 Å
B:20	A:109	2.418 Å
B:20	A:111	2.581 Å
B:21	A:60	2.766 Å
B:21	A:64	4.102 Å
B:22	A:60	4.348 Å
B:22	A:64	2.459 Å

Downloads and reproducibility

JSON PDB Contact table Round observations Figure 4

Execution, model and parameter identities

{
  "checkpoint": {
    "byte_size": 2286561469,
    "path": "boltz2_conf.ckpt",
    "sha256": "090e82ac8c92f5e943fa1b39e7410a44027bea7243c0bbb3caa67a77fc1428e1"
  },
  "completed_at_utc": "2026-10-15T17:30:26.146507+00:00",
  "database_cache_modified": false,
  "determinism_claim": "Fixed seed and captured runtime; bitwise determinism not asserted",
  "device": "NVIDIA GeForce RTX 3070",
  "elapsed_seconds": 43.63591941073537,
  "format": "panapta-bounded-saa-run/v1",
  "input": {
    "byte_size": 374,
    "path": "input.yaml",
    "sha256": "9185f9cda62e14599f3802202d337896d24071de09a6d564854869a96a25a3d2"
  },
  "logs": [
    {
      "byte_size": 470,
      "path": "stdout.log",
      "sha256": "ad856551fa77b2b4769fd907d6b59a6b8e157fa3b1ec2183dec26c44b8e9e8f4"
    },
    {
      "byte_size": 2095,
      "path": "stderr.log",
      "sha256": "a781795778a8891f4bbb0b297b966647218b2a1bf2164c29a65bed8a2ad0f00b"
    }
  ],
  "msa": {
    "byte_size": 215118,
    "path": "protein_msa.csv",
    "sha256": "ef4f064fcf70117e705e3f179361f14d8bc1f2149adbcc4be7e068585854362f"
  },
  "package_source_manifest": {
    "byte_size": 20156,
    "path": "boltz-source-manifest.json",
    "sha256": "a849b41b5d6653ef5dcd38a307ee047b4c796bf7700d1d169d898e9775bda673"
  },
  "return_code": 0,
  "runtime_hparams": {
    "byte_size": 4146,
    "path": "boltz-runtime-hparams.yaml",
    "sha256": "d67d0805a8655c5c4700c9e7383e6a1e9de350a1fce8010d65ae213c02197055"
  },
  "seed": 20261016,
  "settings": {
    "diffusion_samples": 1,
    "max_msa_seqs": 128,
    "max_parallel_samples": 1,
    "model": "boltz2",
    "no_kernels": true,
    "num_subsampled_msa": 128,
    "num_workers": 0,
    "output_format": "pdb",
    "recycling_steps": 3,
    "sampling_steps": 200,
    "use_msa_server": false,
    "use_potentials": true
  },
  "software": {
    "boltz": "2.2.1",
    "cuda": "13.0",
    "python": "3.11.15 | packaged by conda-forge | (main, Mar  5 2026, 16:45:40) [GCC 14.3.0]",
    "torch": "2.12.0+cu130"
  },
  "software_lock": {
    "byte_size": 1883,
    "path": "software-lock.txt",
    "sha256": "4a1c0308246414c11cd354c72bf5e7da7ca30b1e03bfbc866456affac8adff27"
  },
  "started_at_utc": "2026-10-15T17:29:30.024643+00:00",
  "status": "completed"
}