fold_all_atom

(ESMFold2) Folds molecular complexes containing proteins, dna, rna, and ligands. Defaults to esmfold2-fast-2026-05 if no model is given

curl --request POST \
  --url https://biohub.ai/api/v1/fold_all_atom \
  --header 'Authorization: Bearer <token>' \
  --header 'Content-Type: application/json' \
  --data '
{
  "potential_sequence_of_concern": false,
  "sequence": "<string>",
  "msa": {
    "sequences": [
      "<string>"
    ],
    "deletions": [
      [
        123
      ]
    ]
  },
  "num_loops": 20,
  "num_sampling_steps": 100,
  "lm_dropout": 0.3,
  "lm_mask_pct": 0,
  "msa_max_depth": 1024,
  "msa_column_mask_rate": 0.1,
  "include_distogram": false,
  "include_pae": false,
  "include_pair_chains_iptm": false,
  "all_atom_input": {
    "sequences": [
      {
        "sequence": "<string>",
        "type": "protein",
        "id": "<string>",
        "msa": {
          "sequences": [
            "<string>"
          ],
          "deletions": [
            [
              123
            ]
          ]
        },
        "modifications": [
          {
            "position": 123,
            "ccd": "<string>"
          }
        ]
      }
    ],
    "covalent_bonds": [
      {
        "chain_id1": "<string>",
        "res_idx1": 123,
        "atom_idx1": 123,
        "chain_id2": "<string>",
        "res_idx2": 123,
        "atom_idx2": 123
      }
    ],
    "pocket": {
      "binder_chain_id": "<string>",
      "contacts": [
        [
          "<string>",
          123
        ]
      ]
    },
    "distogram_conditioning": [
      {
        "chain_id": "<string>"
      }
    ]
  },
  "include_embeddings": false
}
'

import requests

url = "https://biohub.ai/api/v1/fold_all_atom"

payload = {
    "potential_sequence_of_concern": False,
    "sequence": "<string>",
    "msa": {
        "sequences": ["<string>"],
        "deletions": [[123]]
    },
    "num_loops": 20,
    "num_sampling_steps": 100,
    "lm_dropout": 0.3,
    "lm_mask_pct": 0,
    "msa_max_depth": 1024,
    "msa_column_mask_rate": 0.1,
    "include_distogram": False,
    "include_pae": False,
    "include_pair_chains_iptm": False,
    "all_atom_input": {
        "sequences": [
            {
                "sequence": "<string>",
                "type": "protein",
                "id": "<string>",
                "msa": {
                    "sequences": ["<string>"],
                    "deletions": [[123]]
                },
                "modifications": [
                    {
                        "position": 123,
                        "ccd": "<string>"
                    }
                ]
            }
        ],
        "covalent_bonds": [
            {
                "chain_id1": "<string>",
                "res_idx1": 123,
                "atom_idx1": 123,
                "chain_id2": "<string>",
                "res_idx2": 123,
                "atom_idx2": 123
            }
        ],
        "pocket": {
            "binder_chain_id": "<string>",
            "contacts": [["<string>", 123]]
        },
        "distogram_conditioning": [{ "chain_id": "<string>" }]
    },
    "include_embeddings": False
}
headers = {
    "Authorization": "Bearer <token>",
    "Content-Type": "application/json"
}

response = requests.post(url, json=payload, headers=headers)

print(response.text)

const options = {
  method: 'POST',
  headers: {Authorization: 'Bearer <token>', 'Content-Type': 'application/json'},
  body: JSON.stringify({
    potential_sequence_of_concern: false,
    sequence: '<string>',
    msa: {sequences: ['<string>'], deletions: [[123]]},
    num_loops: 20,
    num_sampling_steps: 100,
    lm_dropout: 0.3,
    lm_mask_pct: 0,
    msa_max_depth: 1024,
    msa_column_mask_rate: 0.1,
    include_distogram: false,
    include_pae: false,
    include_pair_chains_iptm: false,
    all_atom_input: {
      sequences: [
        {
          sequence: '<string>',
          type: 'protein',
          id: '<string>',
          msa: {sequences: ['<string>'], deletions: [[123]]},
          modifications: [{position: 123, ccd: '<string>'}]
        }
      ],
      covalent_bonds: [
        {
          chain_id1: '<string>',
          res_idx1: 123,
          atom_idx1: 123,
          chain_id2: '<string>',
          res_idx2: 123,
          atom_idx2: 123
        }
      ],
      pocket: {binder_chain_id: '<string>', contacts: [['<string>', 123]]},
      distogram_conditioning: [{chain_id: '<string>'}]
    },
    include_embeddings: false
  })
};

fetch('https://biohub.ai/api/v1/fold_all_atom', options)
  .then(res => res.json())
  .then(res => console.log(res))
  .catch(err => console.error(err));

<?php

$curl = curl_init();

curl_setopt_array($curl, [
  CURLOPT_URL => "https://biohub.ai/api/v1/fold_all_atom",
  CURLOPT_RETURNTRANSFER => true,
  CURLOPT_ENCODING => "",
  CURLOPT_MAXREDIRS => 10,
  CURLOPT_TIMEOUT => 30,
  CURLOPT_HTTP_VERSION => CURL_HTTP_VERSION_1_1,
  CURLOPT_CUSTOMREQUEST => "POST",
  CURLOPT_POSTFIELDS => json_encode([
    'potential_sequence_of_concern' => false,
    'sequence' => '<string>',
    'msa' => [
        'sequences' => [
                '<string>'
        ],
        'deletions' => [
                [
                                123
                ]
        ]
    ],
    'num_loops' => 20,
    'num_sampling_steps' => 100,
    'lm_dropout' => 0.3,
    'lm_mask_pct' => 0,
    'msa_max_depth' => 1024,
    'msa_column_mask_rate' => 0.1,
    'include_distogram' => false,
    'include_pae' => false,
    'include_pair_chains_iptm' => false,
    'all_atom_input' => [
        'sequences' => [
                [
                                'sequence' => '<string>',
                                'type' => 'protein',
                                'id' => '<string>',
                                'msa' => [
                                                                'sequences' => [
                                                                                                                                '<string>'
                                                                ],
                                                                'deletions' => [
                                                                                                                                [
                                                                                                                                                                                                                                                                123
                                                                                                                                ]
                                                                ]
                                ],
                                'modifications' => [
                                                                [
                                                                                                                                'position' => 123,
                                                                                                                                'ccd' => '<string>'
                                                                ]
                                ]
                ]
        ],
        'covalent_bonds' => [
                [
                                'chain_id1' => '<string>',
                                'res_idx1' => 123,
                                'atom_idx1' => 123,
                                'chain_id2' => '<string>',
                                'res_idx2' => 123,
                                'atom_idx2' => 123
                ]
        ],
        'pocket' => [
                'binder_chain_id' => '<string>',
                'contacts' => [
                                [
                                                                '<string>',
                                                                123
                                ]
                ]
        ],
        'distogram_conditioning' => [
                [
                                'chain_id' => '<string>'
                ]
        ]
    ],
    'include_embeddings' => false
  ]),
  CURLOPT_HTTPHEADER => [
    "Authorization: Bearer <token>",
    "Content-Type: application/json"
  ],
]);

$response = curl_exec($curl);
$err = curl_error($curl);

curl_close($curl);

if ($err) {
  echo "cURL Error #:" . $err;
} else {
  echo $response;
}

package main

import (
	"fmt"
	"strings"
	"net/http"
	"io"
)

func main() {

	url := "https://biohub.ai/api/v1/fold_all_atom"

	payload := strings.NewReader("{\n  \"potential_sequence_of_concern\": false,\n  \"sequence\": \"<string>\",\n  \"msa\": {\n    \"sequences\": [\n      \"<string>\"\n    ],\n    \"deletions\": [\n      [\n        123\n      ]\n    ]\n  },\n  \"num_loops\": 20,\n  \"num_sampling_steps\": 100,\n  \"lm_dropout\": 0.3,\n  \"lm_mask_pct\": 0,\n  \"msa_max_depth\": 1024,\n  \"msa_column_mask_rate\": 0.1,\n  \"include_distogram\": false,\n  \"include_pae\": false,\n  \"include_pair_chains_iptm\": false,\n  \"all_atom_input\": {\n    \"sequences\": [\n      {\n        \"sequence\": \"<string>\",\n        \"type\": \"protein\",\n        \"id\": \"<string>\",\n        \"msa\": {\n          \"sequences\": [\n            \"<string>\"\n          ],\n          \"deletions\": [\n            [\n              123\n            ]\n          ]\n        },\n        \"modifications\": [\n          {\n            \"position\": 123,\n            \"ccd\": \"<string>\"\n          }\n        ]\n      }\n    ],\n    \"covalent_bonds\": [\n      {\n        \"chain_id1\": \"<string>\",\n        \"res_idx1\": 123,\n        \"atom_idx1\": 123,\n        \"chain_id2\": \"<string>\",\n        \"res_idx2\": 123,\n        \"atom_idx2\": 123\n      }\n    ],\n    \"pocket\": {\n      \"binder_chain_id\": \"<string>\",\n      \"contacts\": [\n        [\n          \"<string>\",\n          123\n        ]\n      ]\n    },\n    \"distogram_conditioning\": [\n      {\n        \"chain_id\": \"<string>\"\n      }\n    ]\n  },\n  \"include_embeddings\": false\n}")

	req, _ := http.NewRequest("POST", url, payload)

	req.Header.Add("Authorization", "Bearer <token>")
	req.Header.Add("Content-Type", "application/json")

	res, _ := http.DefaultClient.Do(req)

	defer res.Body.Close()
	body, _ := io.ReadAll(res.Body)

	fmt.Println(string(body))

}

HttpResponse<String> response = Unirest.post("https://biohub.ai/api/v1/fold_all_atom")
  .header("Authorization", "Bearer <token>")
  .header("Content-Type", "application/json")
  .body("{\n  \"potential_sequence_of_concern\": false,\n  \"sequence\": \"<string>\",\n  \"msa\": {\n    \"sequences\": [\n      \"<string>\"\n    ],\n    \"deletions\": [\n      [\n        123\n      ]\n    ]\n  },\n  \"num_loops\": 20,\n  \"num_sampling_steps\": 100,\n  \"lm_dropout\": 0.3,\n  \"lm_mask_pct\": 0,\n  \"msa_max_depth\": 1024,\n  \"msa_column_mask_rate\": 0.1,\n  \"include_distogram\": false,\n  \"include_pae\": false,\n  \"include_pair_chains_iptm\": false,\n  \"all_atom_input\": {\n    \"sequences\": [\n      {\n        \"sequence\": \"<string>\",\n        \"type\": \"protein\",\n        \"id\": \"<string>\",\n        \"msa\": {\n          \"sequences\": [\n            \"<string>\"\n          ],\n          \"deletions\": [\n            [\n              123\n            ]\n          ]\n        },\n        \"modifications\": [\n          {\n            \"position\": 123,\n            \"ccd\": \"<string>\"\n          }\n        ]\n      }\n    ],\n    \"covalent_bonds\": [\n      {\n        \"chain_id1\": \"<string>\",\n        \"res_idx1\": 123,\n        \"atom_idx1\": 123,\n        \"chain_id2\": \"<string>\",\n        \"res_idx2\": 123,\n        \"atom_idx2\": 123\n      }\n    ],\n    \"pocket\": {\n      \"binder_chain_id\": \"<string>\",\n      \"contacts\": [\n        [\n          \"<string>\",\n          123\n        ]\n      ]\n    },\n    \"distogram_conditioning\": [\n      {\n        \"chain_id\": \"<string>\"\n      }\n    ]\n  },\n  \"include_embeddings\": false\n}")
  .asString();

require 'uri'
require 'net/http'

url = URI("https://biohub.ai/api/v1/fold_all_atom")

http = Net::HTTP.new(url.host, url.port)
http.use_ssl = true

request = Net::HTTP::Post.new(url)
request["Authorization"] = 'Bearer <token>'
request["Content-Type"] = 'application/json'
request.body = "{\n  \"potential_sequence_of_concern\": false,\n  \"sequence\": \"<string>\",\n  \"msa\": {\n    \"sequences\": [\n      \"<string>\"\n    ],\n    \"deletions\": [\n      [\n        123\n      ]\n    ]\n  },\n  \"num_loops\": 20,\n  \"num_sampling_steps\": 100,\n  \"lm_dropout\": 0.3,\n  \"lm_mask_pct\": 0,\n  \"msa_max_depth\": 1024,\n  \"msa_column_mask_rate\": 0.1,\n  \"include_distogram\": false,\n  \"include_pae\": false,\n  \"include_pair_chains_iptm\": false,\n  \"all_atom_input\": {\n    \"sequences\": [\n      {\n        \"sequence\": \"<string>\",\n        \"type\": \"protein\",\n        \"id\": \"<string>\",\n        \"msa\": {\n          \"sequences\": [\n            \"<string>\"\n          ],\n          \"deletions\": [\n            [\n              123\n            ]\n          ]\n        },\n        \"modifications\": [\n          {\n            \"position\": 123,\n            \"ccd\": \"<string>\"\n          }\n        ]\n      }\n    ],\n    \"covalent_bonds\": [\n      {\n        \"chain_id1\": \"<string>\",\n        \"res_idx1\": 123,\n        \"atom_idx1\": 123,\n        \"chain_id2\": \"<string>\",\n        \"res_idx2\": 123,\n        \"atom_idx2\": 123\n      }\n    ],\n    \"pocket\": {\n      \"binder_chain_id\": \"<string>\",\n      \"contacts\": [\n        [\n          \"<string>\",\n          123\n        ]\n      ]\n    },\n    \"distogram_conditioning\": [\n      {\n        \"chain_id\": \"<string>\"\n      }\n    ]\n  },\n  \"include_embeddings\": false\n}"

response = http.request(request)
puts response.read_body

{
  "model": "esm3-open-2024-03",
  "created": "<string>",
  "potential_sequence_of_concern": false,
  "warning_messages": [
    "<string>"
  ],
  "coordinates": [
    [
      [
        123
      ]
    ]
  ],
  "complex": {},
  "plddt": [
    123
  ],
  "ptm": 123,
  "interface_ptm": 123,
  "pae": [
    [
      123
    ]
  ],
  "pair_chains_iptm": [
    [
      123
    ]
  ],
  "output_embedding_sequence": [
    [
      123
    ]
  ],
  "output_embedding_pair_pooled": [
    [
      123
    ]
  ],
  "residue_index": [
    123
  ],
  "entity_id": [
    123
  ]
}

{
  "detail": [
    {
      "loc": [
        "<string>"
      ],
      "msg": "<string>",
      "type": "<string>",
      "input": "<unknown>",
      "ctx": {}
    }
  ]
}

POST

api

fold_all_atom

(ESMFold2) Folds molecular complexes containing proteins, dna, rna, and ligands. Defaults to esmfold2-fast-2026-05 if no model is given

curl --request POST \
  --url https://biohub.ai/api/v1/fold_all_atom \
  --header 'Authorization: Bearer <token>' \
  --header 'Content-Type: application/json' \
  --data '
{
  "potential_sequence_of_concern": false,
  "sequence": "<string>",
  "msa": {
    "sequences": [
      "<string>"
    ],
    "deletions": [
      [
        123
      ]
    ]
  },
  "num_loops": 20,
  "num_sampling_steps": 100,
  "lm_dropout": 0.3,
  "lm_mask_pct": 0,
  "msa_max_depth": 1024,
  "msa_column_mask_rate": 0.1,
  "include_distogram": false,
  "include_pae": false,
  "include_pair_chains_iptm": false,
  "all_atom_input": {
    "sequences": [
      {
        "sequence": "<string>",
        "type": "protein",
        "id": "<string>",
        "msa": {
          "sequences": [
            "<string>"
          ],
          "deletions": [
            [
              123
            ]
          ]
        },
        "modifications": [
          {
            "position": 123,
            "ccd": "<string>"
          }
        ]
      }
    ],
    "covalent_bonds": [
      {
        "chain_id1": "<string>",
        "res_idx1": 123,
        "atom_idx1": 123,
        "chain_id2": "<string>",
        "res_idx2": 123,
        "atom_idx2": 123
      }
    ],
    "pocket": {
      "binder_chain_id": "<string>",
      "contacts": [
        [
          "<string>",
          123
        ]
      ]
    },
    "distogram_conditioning": [
      {
        "chain_id": "<string>"
      }
    ]
  },
  "include_embeddings": false
}
'

import requests

url = "https://biohub.ai/api/v1/fold_all_atom"

payload = {
    "potential_sequence_of_concern": False,
    "sequence": "<string>",
    "msa": {
        "sequences": ["<string>"],
        "deletions": [[123]]
    },
    "num_loops": 20,
    "num_sampling_steps": 100,
    "lm_dropout": 0.3,
    "lm_mask_pct": 0,
    "msa_max_depth": 1024,
    "msa_column_mask_rate": 0.1,
    "include_distogram": False,
    "include_pae": False,
    "include_pair_chains_iptm": False,
    "all_atom_input": {
        "sequences": [
            {
                "sequence": "<string>",
                "type": "protein",
                "id": "<string>",
                "msa": {
                    "sequences": ["<string>"],
                    "deletions": [[123]]
                },
                "modifications": [
                    {
                        "position": 123,
                        "ccd": "<string>"
                    }
                ]
            }
        ],
        "covalent_bonds": [
            {
                "chain_id1": "<string>",
                "res_idx1": 123,
                "atom_idx1": 123,
                "chain_id2": "<string>",
                "res_idx2": 123,
                "atom_idx2": 123
            }
        ],
        "pocket": {
            "binder_chain_id": "<string>",
            "contacts": [["<string>", 123]]
        },
        "distogram_conditioning": [{ "chain_id": "<string>" }]
    },
    "include_embeddings": False
}
headers = {
    "Authorization": "Bearer <token>",
    "Content-Type": "application/json"
}

response = requests.post(url, json=payload, headers=headers)

print(response.text)

const options = {
  method: 'POST',
  headers: {Authorization: 'Bearer <token>', 'Content-Type': 'application/json'},
  body: JSON.stringify({
    potential_sequence_of_concern: false,
    sequence: '<string>',
    msa: {sequences: ['<string>'], deletions: [[123]]},
    num_loops: 20,
    num_sampling_steps: 100,
    lm_dropout: 0.3,
    lm_mask_pct: 0,
    msa_max_depth: 1024,
    msa_column_mask_rate: 0.1,
    include_distogram: false,
    include_pae: false,
    include_pair_chains_iptm: false,
    all_atom_input: {
      sequences: [
        {
          sequence: '<string>',
          type: 'protein',
          id: '<string>',
          msa: {sequences: ['<string>'], deletions: [[123]]},
          modifications: [{position: 123, ccd: '<string>'}]
        }
      ],
      covalent_bonds: [
        {
          chain_id1: '<string>',
          res_idx1: 123,
          atom_idx1: 123,
          chain_id2: '<string>',
          res_idx2: 123,
          atom_idx2: 123
        }
      ],
      pocket: {binder_chain_id: '<string>', contacts: [['<string>', 123]]},
      distogram_conditioning: [{chain_id: '<string>'}]
    },
    include_embeddings: false
  })
};

fetch('https://biohub.ai/api/v1/fold_all_atom', options)
  .then(res => res.json())
  .then(res => console.log(res))
  .catch(err => console.error(err));

<?php

$curl = curl_init();

curl_setopt_array($curl, [
  CURLOPT_URL => "https://biohub.ai/api/v1/fold_all_atom",
  CURLOPT_RETURNTRANSFER => true,
  CURLOPT_ENCODING => "",
  CURLOPT_MAXREDIRS => 10,
  CURLOPT_TIMEOUT => 30,
  CURLOPT_HTTP_VERSION => CURL_HTTP_VERSION_1_1,
  CURLOPT_CUSTOMREQUEST => "POST",
  CURLOPT_POSTFIELDS => json_encode([
    'potential_sequence_of_concern' => false,
    'sequence' => '<string>',
    'msa' => [
        'sequences' => [
                '<string>'
        ],
        'deletions' => [
                [
                                123
                ]
        ]
    ],
    'num_loops' => 20,
    'num_sampling_steps' => 100,
    'lm_dropout' => 0.3,
    'lm_mask_pct' => 0,
    'msa_max_depth' => 1024,
    'msa_column_mask_rate' => 0.1,
    'include_distogram' => false,
    'include_pae' => false,
    'include_pair_chains_iptm' => false,
    'all_atom_input' => [
        'sequences' => [
                [
                                'sequence' => '<string>',
                                'type' => 'protein',
                                'id' => '<string>',
                                'msa' => [
                                                                'sequences' => [
                                                                                                                                '<string>'
                                                                ],
                                                                'deletions' => [
                                                                                                                                [
                                                                                                                                                                                                                                                                123
                                                                                                                                ]
                                                                ]
                                ],
                                'modifications' => [
                                                                [
                                                                                                                                'position' => 123,
                                                                                                                                'ccd' => '<string>'
                                                                ]
                                ]
                ]
        ],
        'covalent_bonds' => [
                [
                                'chain_id1' => '<string>',
                                'res_idx1' => 123,
                                'atom_idx1' => 123,
                                'chain_id2' => '<string>',
                                'res_idx2' => 123,
                                'atom_idx2' => 123
                ]
        ],
        'pocket' => [
                'binder_chain_id' => '<string>',
                'contacts' => [
                                [
                                                                '<string>',
                                                                123
                                ]
                ]
        ],
        'distogram_conditioning' => [
                [
                                'chain_id' => '<string>'
                ]
        ]
    ],
    'include_embeddings' => false
  ]),
  CURLOPT_HTTPHEADER => [
    "Authorization: Bearer <token>",
    "Content-Type: application/json"
  ],
]);

$response = curl_exec($curl);
$err = curl_error($curl);

curl_close($curl);

if ($err) {
  echo "cURL Error #:" . $err;
} else {
  echo $response;
}

package main

import (
	"fmt"
	"strings"
	"net/http"
	"io"
)

func main() {

	url := "https://biohub.ai/api/v1/fold_all_atom"

	payload := strings.NewReader("{\n  \"potential_sequence_of_concern\": false,\n  \"sequence\": \"<string>\",\n  \"msa\": {\n    \"sequences\": [\n      \"<string>\"\n    ],\n    \"deletions\": [\n      [\n        123\n      ]\n    ]\n  },\n  \"num_loops\": 20,\n  \"num_sampling_steps\": 100,\n  \"lm_dropout\": 0.3,\n  \"lm_mask_pct\": 0,\n  \"msa_max_depth\": 1024,\n  \"msa_column_mask_rate\": 0.1,\n  \"include_distogram\": false,\n  \"include_pae\": false,\n  \"include_pair_chains_iptm\": false,\n  \"all_atom_input\": {\n    \"sequences\": [\n      {\n        \"sequence\": \"<string>\",\n        \"type\": \"protein\",\n        \"id\": \"<string>\",\n        \"msa\": {\n          \"sequences\": [\n            \"<string>\"\n          ],\n          \"deletions\": [\n            [\n              123\n            ]\n          ]\n        },\n        \"modifications\": [\n          {\n            \"position\": 123,\n            \"ccd\": \"<string>\"\n          }\n        ]\n      }\n    ],\n    \"covalent_bonds\": [\n      {\n        \"chain_id1\": \"<string>\",\n        \"res_idx1\": 123,\n        \"atom_idx1\": 123,\n        \"chain_id2\": \"<string>\",\n        \"res_idx2\": 123,\n        \"atom_idx2\": 123\n      }\n    ],\n    \"pocket\": {\n      \"binder_chain_id\": \"<string>\",\n      \"contacts\": [\n        [\n          \"<string>\",\n          123\n        ]\n      ]\n    },\n    \"distogram_conditioning\": [\n      {\n        \"chain_id\": \"<string>\"\n      }\n    ]\n  },\n  \"include_embeddings\": false\n}")

	req, _ := http.NewRequest("POST", url, payload)

	req.Header.Add("Authorization", "Bearer <token>")
	req.Header.Add("Content-Type", "application/json")

	res, _ := http.DefaultClient.Do(req)

	defer res.Body.Close()
	body, _ := io.ReadAll(res.Body)

	fmt.Println(string(body))

}

HttpResponse<String> response = Unirest.post("https://biohub.ai/api/v1/fold_all_atom")
  .header("Authorization", "Bearer <token>")
  .header("Content-Type", "application/json")
  .body("{\n  \"potential_sequence_of_concern\": false,\n  \"sequence\": \"<string>\",\n  \"msa\": {\n    \"sequences\": [\n      \"<string>\"\n    ],\n    \"deletions\": [\n      [\n        123\n      ]\n    ]\n  },\n  \"num_loops\": 20,\n  \"num_sampling_steps\": 100,\n  \"lm_dropout\": 0.3,\n  \"lm_mask_pct\": 0,\n  \"msa_max_depth\": 1024,\n  \"msa_column_mask_rate\": 0.1,\n  \"include_distogram\": false,\n  \"include_pae\": false,\n  \"include_pair_chains_iptm\": false,\n  \"all_atom_input\": {\n    \"sequences\": [\n      {\n        \"sequence\": \"<string>\",\n        \"type\": \"protein\",\n        \"id\": \"<string>\",\n        \"msa\": {\n          \"sequences\": [\n            \"<string>\"\n          ],\n          \"deletions\": [\n            [\n              123\n            ]\n          ]\n        },\n        \"modifications\": [\n          {\n            \"position\": 123,\n            \"ccd\": \"<string>\"\n          }\n        ]\n      }\n    ],\n    \"covalent_bonds\": [\n      {\n        \"chain_id1\": \"<string>\",\n        \"res_idx1\": 123,\n        \"atom_idx1\": 123,\n        \"chain_id2\": \"<string>\",\n        \"res_idx2\": 123,\n        \"atom_idx2\": 123\n      }\n    ],\n    \"pocket\": {\n      \"binder_chain_id\": \"<string>\",\n      \"contacts\": [\n        [\n          \"<string>\",\n          123\n        ]\n      ]\n    },\n    \"distogram_conditioning\": [\n      {\n        \"chain_id\": \"<string>\"\n      }\n    ]\n  },\n  \"include_embeddings\": false\n}")
  .asString();

require 'uri'
require 'net/http'

url = URI("https://biohub.ai/api/v1/fold_all_atom")

http = Net::HTTP.new(url.host, url.port)
http.use_ssl = true

request = Net::HTTP::Post.new(url)
request["Authorization"] = 'Bearer <token>'
request["Content-Type"] = 'application/json'
request.body = "{\n  \"potential_sequence_of_concern\": false,\n  \"sequence\": \"<string>\",\n  \"msa\": {\n    \"sequences\": [\n      \"<string>\"\n    ],\n    \"deletions\": [\n      [\n        123\n      ]\n    ]\n  },\n  \"num_loops\": 20,\n  \"num_sampling_steps\": 100,\n  \"lm_dropout\": 0.3,\n  \"lm_mask_pct\": 0,\n  \"msa_max_depth\": 1024,\n  \"msa_column_mask_rate\": 0.1,\n  \"include_distogram\": false,\n  \"include_pae\": false,\n  \"include_pair_chains_iptm\": false,\n  \"all_atom_input\": {\n    \"sequences\": [\n      {\n        \"sequence\": \"<string>\",\n        \"type\": \"protein\",\n        \"id\": \"<string>\",\n        \"msa\": {\n          \"sequences\": [\n            \"<string>\"\n          ],\n          \"deletions\": [\n            [\n              123\n            ]\n          ]\n        },\n        \"modifications\": [\n          {\n            \"position\": 123,\n            \"ccd\": \"<string>\"\n          }\n        ]\n      }\n    ],\n    \"covalent_bonds\": [\n      {\n        \"chain_id1\": \"<string>\",\n        \"res_idx1\": 123,\n        \"atom_idx1\": 123,\n        \"chain_id2\": \"<string>\",\n        \"res_idx2\": 123,\n        \"atom_idx2\": 123\n      }\n    ],\n    \"pocket\": {\n      \"binder_chain_id\": \"<string>\",\n      \"contacts\": [\n        [\n          \"<string>\",\n          123\n        ]\n      ]\n    },\n    \"distogram_conditioning\": [\n      {\n        \"chain_id\": \"<string>\"\n      }\n    ]\n  },\n  \"include_embeddings\": false\n}"

response = http.request(request)
puts response.read_body

{
  "model": "esm3-open-2024-03",
  "created": "<string>",
  "potential_sequence_of_concern": false,
  "warning_messages": [
    "<string>"
  ],
  "coordinates": [
    [
      [
        123
      ]
    ]
  ],
  "complex": {},
  "plddt": [
    123
  ],
  "ptm": 123,
  "interface_ptm": 123,
  "pae": [
    [
      123
    ]
  ],
  "pair_chains_iptm": [
    [
      123
    ]
  ],
  "output_embedding_sequence": [
    [
      123
    ]
  ],
  "output_embedding_pair_pooled": [
    [
      123
    ]
  ],
  "residue_index": [
    123
  ],
  "entity_id": [
    123
  ]
}

{
  "detail": [
    {
      "loc": [
        "<string>"
      ],
      "msg": "<string>",
      "type": "<string>",
      "input": "<unknown>",
      "ctx": {}
    }
  ]
}

This operation accepts inputs up to 768 tokens. For asynchronous predictions, and for inputs up to 4096 tokens, use Batch folding with endpoint: "fold_all_atom".

Authorizations

Authorization

string

header

required

Bearer authentication header of the form Bearer <token>, where <token> is your auth token.

Body

application/json

model

enum<string> | null

You may have access to additional, private models as well. These will be visible on the Rate Limits page under the Developer Console

Available options:

esmfold2-fast-2026-05,

esmfold2-2026-05,

esmfold2-2026-05-cutoff-2025,

null

potential_sequence_of_concern

boolean

default:false

Disclose potential sequences of concern. For approved users, such sequences will not go through additional safety filtering. Reach out if you are interested in using this.

sequence

string | null

Input sequence to be folded.

msa

object | null

MSA data for the query sequence.

Show child attributes

num_loops

integer

default:20

Number of trunk loops for iterative refinement.

Required range: 0 <= x <= 20

num_sampling_steps

integer

default:100

Diffusion ODE solver steps. Lower for speed, higher for quality.

Required range: 1 <= x <= 100

lm_dropout

number

default:0.3

Dropout probability on LM pair embeddings. When > 0, dropout is applied.

Required range: 0 <= x <= 1

lm_mask_pct

number

default:0

Fraction of sequence residues randomly masked before the PLM backbone. If not provided, defaults to 0.1 for ESMFOLD2_FAST and 0.0 for ESMFOLD2

Required range: 0 <= x <= 1

msa_max_depth

integer | null

default:1024

Number of MSA rows randomly subsampled each loop. Set to null to disable (sets msa_subsample_at_inference to False).

Required range: 1 <= x <= 16384

msa_column_mask_rate

number

default:0.1

Fraction of MSA columns randomly masked in non-query rows for inference-time diversity.

Required range: 0 <= x <= 1

include_distogram

boolean

default:false

Whether to include distogram predictions in the response.

include_pae

boolean

default:false

Whether to include Predicted Aligned Error (PAE) matrix in the response.

include_pair_chains_iptm

boolean

default:false

Whether to include pair-chain IPTM predictions in the response.

all_atom_input

object | null

All atom input (protein, RNA, DNA, and ligand) to fold. If provided, performs all-atom folding and ignores the sequence and msa inputs.

Show child attributes

include_embeddings

boolean

default:false

Whether to include sequence and pair embeddings in the response.

Response

Successful Response

model

enum<string>

required

You may have access to additional, private models as well. These will be visible on the Rate Limits page under the Developer Console

Available options:

esm3-open-2024-03,

esmfold2-fast-2026-05,

esmfold2-2026-05,

esmfold2-2026-05-cutoff-2025

created

string

required

ISO formatted date time

potential_sequence_of_concern

boolean

default:false

Indicate that the returned sequence may be of potential concerns.

warning_messages

string[] | null

Warning messages returned by FastAPI.

coordinates

(((number | null)[])[])[] | null

Coordinates of the N, CA, C atom sequence as a Nx37x3 array.

complex

object | null

Molecular complex with support for proteins, nucleic acids, and ligands.

plddt

number[] | null

Per position plddt predictions for a protein or molecular complex. Usually produced by structure decoder.

ptm

number | null

Predicted TM score of a protein or molecular complex. Usually produced by structure decoder.

interface_ptm

number | null

Interface TM score of a protein or molecular complex.

pae

number[][] | null

Predicted Aligned Error matrix for the protein or molecular complex. Shape is L x L. Values are rounded to 2 decimals (well within 0.5 A bin width)

pair_chains_iptm

number[][] | null

Pair-chain IPTM predictions for a protein. Shape is C x C, where C is the number of chains in the protein.

output_embedding_sequence

number[][] | null

Output embedding sequence from the model. Only present if requested.

output_embedding_pair_pooled

number[][] | null

Output embedding pair mean-pooled from the model. Only present if requested.

residue_index

integer[] | null

Residue indexes from the model. Only present if embeddings are requested.

entity_id

integer[] | null

Entity ids (e.g. chain ids) from the model. Only present if embeddings are requested.

Protein Models

Batch API

ESM Atlas

Authorizations

Body

Response