--- title: "(ESMFold2) Folds molecular complexes containing proteins, dna, rna, and ligands. Defaults to esmfold2-fast-2026-05 if no model is given" method: POST path: "/api/v1/fold_all_atom" tags: ["v1"] --- # (ESMFold2) Folds molecular complexes containing proteins, dna, rna, and ligands. Defaults to esmfold2-fast-2026-05 if no model is given `POST /api/v1/fold_all_atom` ## Request - Base URL: `https://dev.evolutionaryscale.ai` (the document declares no server; this is the origin it was published from) - URL: `https://dev.evolutionaryscale.ai/api/v1/fold_all_atom` - Auth: HTTP bearer ## Request body - FoldAllAtomRequest - `model` 'esmfold2-fast-2026-05' | 'esmfold2-2026-05' | 'null', nullable: You may have access to additional, private models as well. These will be visible on the Rate Limits page under the Developer Console - `potential_sequence_of_concern` boolean: 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, nullable: Input sequence to be folded; '|' separates chains. The server names the chains A, B, C in the order they appear. - `msa` union: MSA data for the query sequence. - MSA - `sequences` string[], required - `headers` string[], nullable: Optional alignment headers, including pairing keys. - `deletions` array[], nullable: Optional per-(row, match-column) a3m deletion counts, shape (depth, query match columns). Derived from the insertions when absent. - number[] - string - `num_loops` integer: Number of trunk loops for iterative refinement. - `num_sampling_steps` integer: Diffusion ODE solver steps. Lower for speed, higher for quality. - `lm_dropout` number: Dropout probability on LM pair embeddings. When > 0, dropout is applied. - `lm_mask_pct` number: 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 - `msa_max_depth` integer, nullable: Number of MSA rows randomly subsampled each loop. Set to null to disable (sets msa_subsample_at_inference to False). - `msa_column_mask_rate` number: Fraction of MSA columns randomly masked in non-query rows for inference-time diversity. - `include_distogram` boolean: Whether to include distogram predictions in the response. - `include_pae` boolean: Whether to include Predicted Aligned Error (PAE) matrix in the response. - `include_pair_chains_iptm` boolean: Whether to include pair-chain IPTM predictions in the response. - `all_atom_input` FoldAllAtomInput - `sequences` union[], required - union - ProteinInput - `id` union - string - string[] - `sequence` string, required - `msa` union - MSA - … - string - `modifications` Modification[], nullable - `position` integer, required: Zero-indexed position in the sequence where modification should be applied. - `ccd` string, required: Chemical Component Dictionary (CCD) code for the modification. - `type` 'protein', required - RNAInput - `id` union - string - string[] - `sequence` string, required - `modifications` Modification[], nullable - `position` integer, required: Zero-indexed position in the sequence where modification should be applied. - `ccd` string, required: Chemical Component Dictionary (CCD) code for the modification. - `type` 'rna', required - DNAInput - `id` union - string - string[] - `sequence` string, required - `modifications` Modification[], nullable - `position` integer, required: Zero-indexed position in the sequence where modification should be applied. - `ccd` string, required: Chemical Component Dictionary (CCD) code for the modification. - `type` 'dna', required - LigandInput - `id` union - string - string[] - `smiles` string, nullable - `ccd` string[], nullable - `type` 'ligand', required - `covalent_bonds` CovalentBond[], nullable: List of covalent bonds between chains in the molecular complex. - `chain_id1` string, required: First chain ID in the covalent bond. - `res_idx1` integer, required: Residue index in the first chain. - `atom_idx1` integer, required: Atom index in the first residue. - `chain_id2` string, required: Second chain ID in the covalent bond. - `res_idx2` integer, required: Residue index in the second chain. - `atom_idx2` integer, required: Atom index in the second residue. - `pocket` PocketConditioning - `binder_chain_id` string, required: Chain ID of the binder. - `contacts` array[], required: List of contacts as tuples of (chain_id, residue_index). - unknown[] - unknown - `distogram_conditioning` DistogramConditioning[], nullable: List of distogram conditioning for chains. - `chain_id` string, required: Chain ID for distogram conditioning. - `include_embeddings` boolean: Whether to include sequence and pair embeddings in the response. ## Response `200` Successful Response - FoldResponse - `model` 'esm3-open-2024-03' | 'esmfold2-fast-2026-05' | 'esmfold2-2026-05', required: You may have access to additional, private models as well. These will be visible on the Rate Limits page under the Developer Console - `created` string, required: ISO formatted date time - `potential_sequence_of_concern` boolean: Indicate that the returned sequence may be of potential concerns. - `warning_messages` string[], nullable: Warning messages returned by FastAPI. - `sequence` string, nullable: Folded protein sequence in coordinate order. Always populated by /fold; null for all-atom folding. - `coordinates` array[], nullable: Coordinates of the N, CA, C atom sequence as a Nx37x3 array. - array[] - number[] - `complex` object, nullable: Molecular complex with support for proteins, nucleic acids, and ligands. - `plddt` number[], nullable: Per position plddt predictions for a protein or molecular complex. Usually produced by structure decoder. A multi-chain sequence carries one slot per chain separator, reported as null: those positions are not residues and have no confidence. Drop them before taking a mean. - `ptm` number, nullable: Predicted TM score of a protein or molecular complex. Usually produced by structure decoder. - `interface_ptm` number, nullable: Interface TM score of a protein or molecular complex. - `pae` array[], nullable: 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) - number[] - `pair_chains_iptm` array[], nullable: Pair-chain IPTM predictions for a protein. Shape is C x C, where C is the number of chains in the protein. - number[] - `output_embedding_sequence` array[], nullable: Output embedding sequence from the model. Only present if requested. - number[] - `output_embedding_pair_pooled` array[], nullable: Output embedding pair mean-pooled from the model. Only present if requested. - number[] - `residue_index` integer[], nullable: Residue indexes from the model. Only present if embeddings are requested. - `entity_id` integer[], nullable: Entity ids (e.g. chain ids) from the model. Only present if embeddings are requested. ## Other responses - `422`: Validation Error ## Changes - **2026-10-14** `28a490b11fe1`: 1 info - added the optional property `sequence` to the response with the `200` status - **2026-10-03** `2b39e86ec871`: 2 info - added the new optional request property `all_atom_input/anyOf[#/components/schemas/FoldAllAtomInput]/sequences/items/oneOf[#/components/schemas/ProteinInput]/msa/anyOf[#/components/schemas/MSA]/headers` - added the new optional request property `msa/anyOf[#/components/schemas/MSA]/headers` - **2026-09-03** `422e4d05cd6d`: 2 info - added `subschema #2` to the `all_atom_input/anyOf[#/components/schemas/FoldAllAtomInput]/sequences/items/oneOf[#/components/schemas/ProteinInput]/msa` request property `anyOf` list - added `subschema #2` to the `msa` request property `anyOf` list - **2026-08-26** `b19c9a405304`: 1 breaking - response property `plddt/anyOf[subschema #1]/items/` list-of-types was widened by adding types `null` to media type `application/json` of response `200` [Operation history](https://skmtc.dev/evolutionaryscale/apis/evolutionaryscale-api/changes/api/v1/fold_all_atom/post.md) --- [API](https://skmtc.dev/evolutionaryscale/apis/evolutionaryscale-api.md) - [All operations](https://skmtc.dev/evolutionaryscale/apis/evolutionaryscale-api/llms.txt) - [OpenAPI document](https://skmtc.dev/evolutionaryscale/apis/evolutionaryscale-api/revisions/28a490b11fe1?raw)