> This page is for OpenFold2, version 2.6.0 (Latest) (default). > For other versions, use one of these documentation indexes: > - 2.6.0 (Latest) (default): https://docs.nvidia.com/nim/bionemo/openfold2/2.6.0/llms.txt > - 2.5.0: https://docs.nvidia.com/nim/bionemo/openfold2/2.5.0/llms.txt > - 2.4.0: https://docs.nvidia.com/nim/bionemo/openfold2/2.4.0/llms.txt > - 2.3.0: https://docs.nvidia.com/nim/bionemo/openfold2/2.3.0/llms.txt > - 2.2.0: https://docs.nvidia.com/nim/bionemo/openfold2/2.2.0/llms.txt > - 2.1.0: https://docs.nvidia.com/nim/bionemo/openfold2/2.1.0/llms.txt > - 2.0.0: https://docs.nvidia.com/nim/bionemo/openfold2/2.0.0/llms.txt > - 1.2.0: https://docs.nvidia.com/nim/bionemo/openfold2/1.2.0/llms.txt > - 1.1.0: https://docs.nvidia.com/nim/bionemo/openfold2/1.1.0/llms.txt > - 1.0.0: https://docs.nvidia.com/nim/bionemo/openfold2/1.0.0/llms.txt > For clean Markdown of any page, append .md to the page URL. > For a complete documentation index, see https://docs.nvidia.com/nim/bionemo/llms.txt. > For AI client integration (Claude Code, Cursor, etc.), connect to the MCP server at https://docs.nvidia.com/nim/bionemo/_mcp/server. # Example Requests OpenFold2 NIM provides the following endpoint: - `biology/openfold/openfold2/predict-structure-from-msa-and-template`: Perform structure prediction from an input MSA and templates. Starting with version 2.0.0, only mmCIF-based templates are supported. For information on migrating from HHR-based templates, refer to the [Migration Guide](/nim/bionemo/openfold2/migrating-from-hhr-to-explicit-templates). ## Use the OpenFold2 NIM This section provides real examples of requests that should run when the NIM is correctly configured. We do not recommend submitting requests to this endpoint using curl, because its inputs have characters that require careful escaping in `bash`. We recommend interacting with this endpoint using the Python `requests` module. ### Predict Structure The endpoint accepts requests where the data is formatted as in the [OpenAPI Specification](https://docs.nvidia.com/nim/bionemo/openfold2/2.6.0/api-reference/nim-api-post-call-monomer-structure-from-msa-and-template-biology-openfold-openfold-2-predict-structure-from-msa-and-template-post) Here is an example request using the Python `requests` module. - The field `sequence` is required. - The field `input_id` is optional but recommended. It serves as a unique identifier for tracking requests and correlating responses. Use formats like `"7WBN_A"` (PDB ID + chain) or custom names like `"my_protein_001"`. - The field `alignments` is optional, but omission can result in inaccurate structures. If included, the MSA content must be in `a3m` format. - The field `selected_models` is optional, but included here to reduce runtime, because the default specifies 5 models. - To include templates, set `use_templates`=`True` and populate the `explicit_templates` field with the content of one or more structure files in mmCIF format. Template features are not used if `use_templates`=`False`. The following workflow is recommended when predicting structures for a given protein sequence: 1. Use MSA tools (for example, HHblits, MMseqs2, or ColabFold) to produce multiple sequence alignments and format them in the `a3m` format. 2. Obtain structural templates in **mmCIF** format from sources such as: - PDB database downloads - Experimental structures - Computational models, such as AlphaFold predictions 3. Load the `a3m` files and `mmcif` files in a Python script, and format the request as specified in the OpenAPI specifications. For detailed guidance on migrating from HHR-based templates to mmCIF format, refer to the [Migration Guide](/nim/bionemo/openfold2/migrating-from-hhr-to-explicit-templates). ```python import requests import json # -------------------------------- # parameters # -------------------------------- url = "http://localhost:8000/biology/openfold/openfold2/predict-structure-from-msa-and-template" headers = {"Content-Type": "application/json"} sequence = ( "GGSKENEISHHAKEIERLQKEIERHKQSIKKLKQSEQSNPPPNP" "EGTRQARRNRRRRWRERQRQKENEISHHAKEIERLQKEIERHKQSIKKLKQSEC" ) uniref90_alignment_in_a3m_trunc10=\ """>BQXYMDHSRWGGVPIWVK GGSKENEISHHAKEIERLQKEIERHKQSIKKLKQSEQSNPPPNPEGTRQARRNRRRRWRERQRQKENEISHHAKEIERLQKEIERHKQSIKKLKQSEC >UniRef90_A0A221IUG4 --------------------------QTVKLVKRLYQSNPPPNPEGTRQARRNRRRRWRERQRQ---------------------------------- >UniRef90_A7KWE0 ---------------------------TVRLIKQLYQSNPPPNPEGTRQARRNRRRRWRERQRQ---------------------------------- >UniRef90_A0A2I6UE91 ---------------------------TVKLIKEIYQSNPPPNPEGTRQARRNRRRRWRERQRQ---------------------------------- >UniRef90_D6NY33 ---------------------------AVRLIKQIYQSNPPPNPEGTRQARRNRRRRWRERQRQ---------------------------------- >UniRef90_A0A221IUJ5 --------------------------QTVKLIKRLYQSNPPPNPEGTRQARRNRRRRWREKQRQ---------------------------------- >UniRef90_D6NYR3 ---------------------------TVRLVKQLYQSNPPPNPEGTRQARRNRRRRWRERQRQ---------------------------------- >UniRef90_I6Y2C4 ---------------------------TVRLIKRIYQSNPPPNPEGTRQARRNRRRRWRERQRQIQN------------------------------- >UniRef90_A0A161CVP3 --------------------------QTIRLIKLLYQSNPPPNPEGTRQARRNRRRRWRERQRQ---------------------------------- >UniRef90_Q6EFX9 --------------------------QTVRLIKLLYQSNPPPNPEGTRQARRNRRRRWRERQRQ---------------------------------- >UniRef90_A0A2I6UAR5 --------------------------ETVKIIKYLYQSNPPPNPEGTRQARRNRRRRWRERQRQ---------------------------------- """ small_bfd_alignment_in_a3m = \ """>BQXYMDHSRWGGVPIWVK GGSKENEISHHAKEIERLQKEIERHKQSIKKLKQSEQSNPPPNPEGTRQARRNRRRRWRERQRQKENEISHHAKEIERLQKEIERHKQSIKKLKQSEC >A0A076V4A1_9HIV1 ------------------------------------QSNPPPNHEGTRQARRNRRRRWRERQRQ---------------------------------- """ # Example mmCIF template string (very small, minimal but valid) mmcif_template = """data_SIMPLE # _entry.id SIMPLE # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _chem_comp.id _chem_comp.type GLY 'L-peptide linking' SER 'L-peptide linking' LYS 'L-peptide linking' GLU 'L-peptide linking' ASN 'L-peptide linking' ILE 'L-peptide linking' # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id 1 1 GLY 1 2 GLY 1 3 SER 1 4 LYS 1 5 GLU 1 6 ASN 1 7 GLU 1 8 ILE # loop_ _struct_asym.id _struct_asym.entity_id A 1 # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 N N . GLY A 1 1 ? 0.000 0.000 0.000 1.00 20.00 ? 1 GLY A N 1 ATOM 2 C CA . GLY A 1 1 ? 1.458 0.000 0.000 1.00 20.00 ? 1 GLY A CA 1 ATOM 3 C C . GLY A 1 1 ? 2.009 1.420 0.000 1.00 20.00 ? 1 GLY A C 1 ATOM 4 O O . GLY A 1 1 ? 1.251 2.389 0.000 1.00 20.00 ? 1 GLY A O 1 ATOM 5 N N . GLY A 1 2 ? 3.200 1.650 0.000 1.00 20.00 ? 2 GLY A N 1 ATOM 6 C CA . GLY A 1 2 ? 3.658 3.030 0.000 1.00 20.00 ? 2 GLY A CA 1 ATOM 7 C C . GLY A 1 2 ? 5.116 3.260 0.000 1.00 20.00 ? 2 GLY A C 1 ATOM 8 O O . GLY A 1 2 ? 5.874 2.291 0.000 1.00 20.00 ? 2 GLY A O 1 ATOM 9 N N . SER A 1 3 ? 5.574 4.640 0.000 1.00 20.00 ? 3 SER A N 1 ATOM 10 C CA . SER A 1 3 ? 7.032 4.870 0.000 1.00 20.00 ? 3 SER A CA 1 ATOM 11 C C . SER A 1 3 ? 7.490 6.250 0.000 1.00 20.00 ? 3 SER A C 1 ATOM 12 O O . SER A 1 3 ? 6.732 7.219 0.000 1.00 20.00 ? 3 SER A O 1 ATOM 13 C CB . SER A 1 3 ? 7.532 4.370 1.200 1.00 20.00 ? 3 SER A CB 1 ATOM 14 O OG . SER A 1 3 ? 8.932 4.600 1.200 1.00 20.00 ? 3 SER A OG 1 ATOM 15 N N . LYS A 1 4 ? 8.681 6.480 0.000 1.00 20.00 ? 4 LYS A N 1 ATOM 16 C CA . LYS A 1 4 ? 9.139 7.860 0.000 1.00 20.00 ? 4 LYS A CA 1 ATOM 17 C C . LYS A 1 4 ? 10.597 8.090 0.000 1.00 20.00 ? 4 LYS A C 1 ATOM 18 O O . LYS A 1 4 ? 11.355 7.121 0.000 1.00 20.00 ? 4 LYS A O 1 ATOM 19 C CB . LYS A 1 4 ? 8.639 8.360 1.200 1.00 20.00 ? 4 LYS A CB 1 ATOM 20 C CG . LYS A 1 4 ? 9.139 9.740 1.200 1.00 20.00 ? 4 LYS A CG 1 ATOM 21 C CD . LYS A 1 4 ? 8.639 10.240 2.400 1.00 20.00 ? 4 LYS A CD 1 ATOM 22 C CE . LYS A 1 4 ? 9.139 11.620 2.400 1.00 20.00 ? 4 LYS A CE 1 ATOM 23 N NZ . LYS A 1 4 ? 8.639 12.120 3.600 1.00 20.00 ? 4 LYS A NZ 1 ATOM 24 N N . GLU A 1 5 ? 11.055 9.470 0.000 1.00 20.00 ? 5 GLU A N 1 ATOM 25 C CA . GLU A 1 5 ? 12.513 9.700 0.000 1.00 20.00 ? 5 GLU A CA 1 ATOM 26 C C . GLU A 1 5 ? 12.971 11.080 0.000 1.00 20.00 ? 5 GLU A C 1 ATOM 27 O O . GLU A 1 5 ? 12.213 12.049 0.000 1.00 20.00 ? 5 GLU A O 1 ATOM 28 C CB . GLU A 1 5 ? 13.013 9.200 1.200 1.00 20.00 ? 5 GLU A CB 1 ATOM 29 C CG . GLU A 1 5 ? 14.471 9.430 1.200 1.00 20.00 ? 5 GLU A CG 1 ATOM 30 C CD . GLU A 1 5 ? 14.929 10.810 1.200 1.00 20.00 ? 5 GLU A CD 1 ATOM 31 O OE1 . GLU A 1 5 ? 14.171 11.779 1.200 1.00 20.00 ? 5 GLU A OE1 1 ATOM 32 O OE2 . GLU A 1 5 ? 16.129 10.940 1.200 1.00 20.00 ? 5 GLU A OE2 1 ATOM 33 N N . ASN A 1 6 ? 14.162 11.310 0.000 1.00 20.00 ? 6 ASN A N 1 ATOM 34 C CA . ASN A 1 6 ? 14.620 12.690 0.000 1.00 20.00 ? 6 ASN A CA 1 ATOM 35 C C . ASN A 1 6 ? 16.078 12.920 0.000 1.00 20.00 ? 6 ASN A C 1 ATOM 36 O O . ASN A 1 6 ? 16.836 11.951 0.000 1.00 20.00 ? 6 ASN A O 1 ATOM 37 C CB . ASN A 1 6 ? 14.120 13.190 1.200 1.00 20.00 ? 6 ASN A CB 1 ATOM 38 C CG . ASN A 1 6 ? 14.578 14.570 1.200 1.00 20.00 ? 6 ASN A CG 1 ATOM 39 O OD1 . ASN A 1 6 ? 15.736 14.800 1.200 1.00 20.00 ? 6 ASN A OD1 1 ATOM 40 N ND2 . ASN A 1 6 ? 13.820 15.539 1.200 1.00 20.00 ? 6 ASN A ND2 1 ATOM 41 N N . GLU A 1 7 ? 16.536 14.300 0.000 1.00 20.00 ? 7 GLU A N 1 ATOM 42 C CA . GLU A 1 7 ? 17.994 14.530 0.000 1.00 20.00 ? 7 GLU A CA 1 ATOM 43 C C . GLU A 1 7 ? 18.452 15.910 0.000 1.00 20.00 ? 7 GLU A C 1 ATOM 44 O O . GLU A 1 7 ? 17.694 16.879 0.000 1.00 20.00 ? 7 GLU A O 1 ATOM 45 N N . ILE A 1 8 ? 19.643 16.140 0.000 1.00 20.00 ? 8 ILE A N 1 ATOM 46 C CA . ILE A 1 8 ? 20.101 17.520 0.000 1.00 20.00 ? 8 ILE A CA 1 ATOM 47 C C . ILE A 1 8 ? 21.559 17.750 0.000 1.00 20.00 ? 8 ILE A C 1 ATOM 48 O O . ILE A 1 8 ? 22.317 16.781 0.000 1.00 20.00 ? 8 ILE A O 1 ATOM 49 C CB . ILE A 1 8 ? 19.601 18.020 1.200 1.00 20.00 ? 8 ILE A CB 1 ATOM 50 C CG1 . ILE A 1 8 ? 18.101 17.790 1.200 1.00 20.00 ? 8 ILE A CG1 1 ATOM 51 C CG2 . ILE A 1 8 ? 20.101 19.400 1.200 1.00 20.00 ? 8 ILE A CG2 1 ATOM 52 C CD1 . ILE A 1 8 ? 17.601 18.290 2.400 1.00 20.00 ? 8 ILE A CD1 1 # """ # -------------------------------- # assemble request content # -------------------------------- data = { "sequence": sequence, "input_id": "example_protein_001", # Optional: unique identifier for request tracking "selected_models": [1, 2], "alignments": { "uniref90": { "a3m": { "alignment": uniref90_alignment_in_a3m_trunc10, "format": "a3m", } }, "small_bfd": { "a3m": { "alignment": small_bfd_alignment_in_a3m, "format": "a3m", } } }, "use_templates": True, "explicit_templates": [ { "structure": mmcif_template, "format": "mmcif", "name": "demo_template", "source": "user_provided" } ], } # -------------------------------- # post-to-server # -------------------------------- response = requests.post( url=url, data=json.dumps(data), headers=headers, timeout=300, ) # Check if the request was successful if response.ok: print("Request succeeded:", response.json()) else: print("Request failed:", response.status_code, response.text) ``` The runtime for structure prediction is impacted by both sequence length and the number of sequences in the multiple sequence alignment. On an `NVIDIA H100 80GB HBM3` device, this example should complete in under 30 seconds. ### Response Fields Starting with version 2.5.0, each predicted structure in `structures_in_ranked_order` includes per-residue and per-residue-pair confidence outputs alongside the structure coordinates. Refer to the [API Reference](https://docs.nvidia.com/nim/bionemo/openfold2/2.6.0/api-reference/nim-api-post-call-monomer-structure-from-msa-and-template-biology-openfold-openfold-2-predict-structure-from-msa-and-template-post) for the full schema. The response is a JSON object with the following top-level fields: - `structures_in_ranked_order`: A list of predicted structures, ordered by descending `confidence`. - `input_id`: Echoes the `input_id` from the request, if supplied. - `metrics`: Optional metrics for the prediction (for example, `relaxation_time_in_seconds`). - `of2_nim_handled_error_message`: `"no-handled-error"` on success. Each entry in `structures_in_ranked_order` is an `OF2StructureRecord` with these fields: | Field | Type | Description | | --- | --- | --- | | `structure` | `string` | Predicted structure file contents (PDB or mmCIF text). | | `format` | `string` | `"pdb"` or `"mmcif"`. | | `relaxed` | `boolean` | `true` if structural relaxation was applied.| | `rank_by_confidence` | `integer` | Zero-based rank, sorted by descending `confidence`. | | `confidence` | `number \| null` | Composite confidence used to rank this structure. | | `model_param_set` | `integer \| null` | Which of the five model parameter sets produced this structure (1–5). | | `plddt` | `array[number] \| null` | **New in 2.5.0.** Per-residue predicted local-distance difference test (pLDDT), one value per residue (range 0–100). | | `predicted_aligned_error` | `array[array[number]] \| null` | **New in 2.5.0.** Per-residue-pair bin probabilities from the predicted-aligned-error head. May be `null` depending on the model profile. | | `max_predicted_aligned_error` | `number \| array \| null` | **New in 2.5.0.** Upper bound of the PAE binning scheme used for this prediction. `null` when the TM head is disabled. | | `aligned_confidence_probs` | `array \| null` | **New in 2.5.0; deprecated in 2.6.0.** Always `null` in 2.6.0 and later. The field remains in the response schema so existing clients do not break on a missing key. Use `predicted_aligned_error` instead. | | `ptm_score` | `number \| null` | **New in 2.5.0.** Predicted TM score for the full structure when the TM confidence head is enabled; `null` otherwise. | #### Example: Read the Confidence Outputs From the Top-Ranked Structure ```python top = response.json()["structures_in_ranked_order"][0] print("rank:", top["rank_by_confidence"], "confidence:", top["confidence"]) print("pTM:", top["ptm_score"]) print("pLDDT (first 5):", top["plddt"][:5]) print("PAE shape:", len(top["predicted_aligned_error"]), "x", len(top["predicted_aligned_error"][0])) ```