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| # JSON file format for AlphaFold Server jobs | ||
|
|
||
| You can | ||
| [download an example JSON file here](https://github.com/google-deepmind/alphafold/blob/main/server/example.json); | ||
| here we describe the contents of this example JSON file. | ||
|
|
||
| This JSON file consists of a list of dictionaries (even in the case of a single | ||
| dictionary, a single-element list must be used), with each dictionary containing | ||
| a job description. Therefore, you can specify multiple jobs in one JSON file. | ||
|
|
||
| Each job description contains a job name, a list of PRNG seeds (which can be an | ||
| empty list for automated random seed assignment), and a list of entities | ||
| (molecules) to be modeled. | ||
|
|
||
| AlphaFold Server JSON files are especially useful for automation of repetitive | ||
| modeling jobs (e.g. to screen interactions of one protein with a small number of | ||
| others). The easiest way to construct an initial JSON file is to run a modeling | ||
| job via AlphaFold Server GUI and use it as a template. AlphaFold Server will | ||
| produce a zip file containing modeling results. Inside the zip file you will | ||
| find a JSON file named `<job_name>_job_request.json` containing the job inputs. | ||
| These files offer a convenient starting point for generating new jobs as they | ||
| are easily editable in standard text editors or in programming environments like | ||
| Google Colab notebooks. | ||
|
|
||
| Note that comments are not allowed in JSON files. | ||
|
|
||
| ## Job name, seeds and sequences | ||
|
|
||
| * `name` is a string with the job name. This is how the job will appear as in | ||
| the job history table. | ||
| * `modelSeeds` is a list of strings of uint32 seed values (e.g. | ||
| `["1593933729", "4273"]`). Seeds are used to run the modeling. We recommend | ||
| providing an empty list, in which case a single random seed will be used. | ||
| This is the recommended option. | ||
| * `sequences` is a list of dictionaries that carry descriptions of the | ||
| entities (molecules) for modeling. | ||
|
|
||
| ```json | ||
| { | ||
| "name": "Test Fold Job Number One", | ||
| "modelSeeds": [], | ||
| "sequences": [...] | ||
| } | ||
| ``` | ||
|
|
||
| ## Entity types | ||
|
|
||
| Valid entity types mirror those available in the AlphaFold Server web interface: | ||
|
|
||
| * `proteinChain` – used for proteins | ||
| * `dnaSequence` – used for DNA (single strand) | ||
| * `rnaSequence` – used for RNA (single strand) | ||
| * `ligand` – used for allowed ligands | ||
| * `ion` – used for allowed ions | ||
|
|
||
| ### Protein chains | ||
|
|
||
| `sequence` is a string containing protein sequence; the same limitations as in | ||
| the UI are in place, e.g. only letters corresponding to amino acids are allowed, | ||
| as defined by IUPAC. Only 20 standard amino acid type are supported. | ||
|
|
||
| `count` is the number of copies of this protein chain (integer). | ||
|
|
||
| `glycans` is an optional list of dictionaries that carries descriptions of the | ||
| protein glycosylation. | ||
|
|
||
| * `residues` is a string defining glycan. Please refer to the | ||
| [FAQ](https://alphafoldserver.com/faq) for the format description and | ||
| allowed glycans. | ||
| * `position` is a position of the amino acid to which the glycan is attached | ||
| (integer, 1-based indexing). | ||
|
|
||
| `modifications` is an optional list of dictionaries that carries descriptions of | ||
| the post-translational modifications. | ||
|
|
||
| * `ptmType` is a string containing the | ||
| [CCD code](https://www.wwpdb.org/data/ccd) of the modification; the same | ||
| codes are allowed as in the UI. | ||
| * `position` is a position of the modified amino acid (integer). | ||
| * Allowed modifications: `CCD_SEP`, `CCD_TPO`, `CCD_PTR`, `CCD_NEP`, | ||
| `CCD_HIP`, `CCD_ALY`, `CCD_MLY`, `CCD_M3L`, `CCD_MLZ`, `CCD_2MR`, `CCD_AGM`, | ||
| `CCD_MCS`, `CCD_HYP`, `CCD_HY3`, `CCD_LYZ`, `CCD_AHB`, `CCD_P1L`, `CCD_SNN`, | ||
| `CCD_SNC`, `CCD_TRF`, `CCD_KCR`, `CCD_CIR`, `CCD_YHA` | ||
|
|
||
| ```json | ||
| { | ||
| "proteinChain": { | ||
| "sequence": "PREACHINGS", | ||
|
|
||
| "glycans": [ | ||
| { | ||
| "residues": "NAG(NAG)(BMA)", | ||
| "position": 8 | ||
| }, | ||
| { | ||
| "residues": "BMA", | ||
| "position": 10 | ||
| } | ||
| ], | ||
|
|
||
| "modifications": [ | ||
| { | ||
| "ptmType": "CCD_HY3", | ||
| "ptmPosition": 1 | ||
| }, | ||
| { | ||
| "ptmType": "CCD_P1L", | ||
| "ptmPosition": 5 | ||
| } | ||
| ], | ||
|
|
||
| "count": 1 | ||
| } | ||
| }, | ||
| { | ||
| "proteinChain": { | ||
| "sequence": "REACHER", | ||
| "count": 1 | ||
| } | ||
| } | ||
| ``` | ||
|
|
||
| ### DNA chains | ||
|
|
||
| Please note that the `dnaSequence` type refers to single stranded DNA. If you | ||
| wish to model double stranded DNA, please add a second `"dnaSequence`", carrying | ||
| the sequence of the reverse complement strand. | ||
|
|
||
| `sequence` is a string containing a DNA sequence; the same limitations as in the | ||
| UI are in place, i.e. only letters A, T, G, C are allowed. | ||
|
|
||
| `count` is a number of copies of this DNA chain (integer). | ||
|
|
||
| `modifications` is an optional list of dictionaries that carries descriptions of | ||
| the DNA chemical modifications. | ||
|
|
||
| * `modificationType` is a string containing | ||
| [CCD code](https://www.wwpdb.org/data/ccd) of modification; the same codes | ||
| are allowed as in the UI. | ||
| * `basePosition` is a position of the modified nucleotide (integer). | ||
| * Allowed modifications: `CCD_5CM`, `CCD_C34`, `CCD_5HC`, `CCD_6OG`, | ||
| `CCD_6MA`, `CCD_1CC`, `CCD_8OG`, `CCD_5FC`, `CCD_3DR` | ||
|
|
||
| ```json | ||
| { | ||
| "dnaSequence": { | ||
| "sequence": "GATTACA", | ||
|
|
||
| "modifications": [ | ||
| { | ||
| "modificationType": "CCD_6OG", | ||
| "basePosition": 1 | ||
| }, | ||
| { | ||
| "modificationType": "CCD_6MA", | ||
| "basePosition": 2 | ||
| } | ||
| ], | ||
|
|
||
| "count": 1 | ||
| } | ||
| }, | ||
| { | ||
| "dnaSequence": { | ||
| "sequence": "TGTAATC", | ||
| "count": 1 | ||
| } | ||
| } | ||
| ``` | ||
|
|
||
| ### RNA chains | ||
|
|
||
| `sequence` is a string containing RNA sequence (single strand); the same | ||
| limitations as in the UI are in place, e.g. only letters A, U, G, C are allowed. | ||
|
|
||
| `count` is a number of copies of this RNA chain (integer). | ||
|
|
||
| `modifications` is an optional list of dictionaries that carries descriptions of | ||
| the RNA chemical modifications. | ||
|
|
||
| * `modificationType` is a string containing | ||
| [CCD code](https://www.wwpdb.org/data/ccd) of modification; the same codes | ||
| are allowed as in the UI. | ||
| * `basePosition` is a position of the modified nucleotide (integer). | ||
| * Allowed modifications: `CCD_PSU`, `CCD_5MC`, `CCD_OMC`, `CCD_4OC`, | ||
| `CCD_5MU`, `CCD_OMU`, `CCD_UR3`, `CCD_A2M`, `CCD_MA6`, `CCD_6MZ`, `CCD_2MG`, | ||
| `CCD_OMG`, `CCD_7MG`, `CCD_RSQ` | ||
|
|
||
| ```json | ||
| { | ||
| "rnaSequence": { | ||
| "sequence": "GUAC", | ||
|
|
||
| "modifications": [ | ||
| { | ||
| "modificationType": "CCD_2MG", | ||
| "basePosition": 1 | ||
| }, | ||
| { | ||
| "modificationType": "CCD_5MC", | ||
| "basePosition": 4 | ||
| } | ||
| ], | ||
|
|
||
| "count": 1 | ||
| } | ||
| } | ||
| ``` | ||
|
|
||
| ### Ligands | ||
|
|
||
| `ligand` is a string containing the [CCD code](https://www.wwpdb.org/data/ccd) | ||
| of the ligand; the same codes are allowed as in the UI. | ||
|
|
||
| `count` is the number of copies of this ligand (integer). | ||
|
|
||
| Allowed ligands: `CCD_ADP`, `CCD_ATP`, `CCD_AMP`, `CCD_GTP`, `CCD_GDP`, | ||
| `CCD_FAD`, `CCD_NAD`, `CCD_NAP`, `CCD_NDP`, `CCD_HEM`, `CCD_HEC`, `CCD_PLM`, | ||
| `CCD_OLA`, `CCD_MYR`, `CCD_CIT`, `CCD_CLA`, `CCD_CHL`, `CCD_BCL`, `CCD_BCB` | ||
|
|
||
| ```json | ||
| { | ||
| "ligand": { | ||
| "ligand": "CCD_ATP", | ||
| "count": 1 | ||
| } | ||
| }, | ||
| { | ||
| "ligand": { | ||
| "ligand": "CCD_HEM", | ||
| "count": 2 | ||
| } | ||
| } | ||
| ``` | ||
|
|
||
| ### Ions | ||
|
|
||
| `ion` is a string containing [CCD code](https://www.wwpdb.org/data/ccd) of the | ||
| ion; the same codes are allowed as in the UI. The ion charge is implicitly | ||
| specified by the CCD code. | ||
|
|
||
| `count` is a number of copies of this ion (integer). | ||
|
|
||
| Allowed ions: `MG`, `ZN`, `CL`, `CA`, `NA`, `MN`, `K`, `FE`, `CU`, `CO` | ||
|
|
||
| ```json | ||
| { | ||
| "ion": { | ||
| "ion": "MG", | ||
| "count": 2 | ||
| } | ||
| }, | ||
| { | ||
| "ion": { | ||
| "ion": "NA", | ||
| "count": 3 | ||
| } | ||
| } | ||
| ``` | ||
|
|
||
| # Additional modeling jobs | ||
|
|
||
| You may specify multiple jobs in one JSON file. This is an example of a simple | ||
| job request for one protein chain and two copies of the palindromic DNA | ||
| sequence: | ||
|
|
||
| ```json | ||
| { | ||
| "name": "Test Fold Job Number Two", | ||
| "modelSeeds": [], | ||
| "sequences": [ | ||
| { | ||
| "proteinChain": { | ||
| "sequence": "TEACHINGS", | ||
| "count": 1 | ||
| } | ||
| }, | ||
| { | ||
| "dnaSequence": { | ||
| "sequence": "TAGCTA", | ||
| "count": 2 | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| ``` |
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