View source for SecStrAnnotator:SecStrAPI

The [https://webchem.ncbr.muni.cz/API/SecStr '''SecStrAPI'''] allows programmatic access to precomputed secondary structure annotations.

== Requests ==

<ul>

<li>
The annotation for a particular PDB entry is accessible by:
<br><code><nowiki>https://webchem.ncbr.muni.cz/API/SecStr/Annotation/{pdbid}</nowiki></code>
<br>Example: 
<br><code>https://webchem.ncbr.muni.cz/API/SecStr/Annotation/1tqn</code>
</li>
<br>

<li>
The list of available PDB entries and the annotated domains in each entry is accessible by:
<br><code>https://webchem.ncbr.muni.cz/API/SecStr/List/Annotation</code>
</li>

</ul>

== SecStrAPI format ==

The annotations are provided in SecStrAPI JSON format, demonstrated below.

<source lang="json">

{
    "api_version": "1.0",                     # pdb-style residue range (auth_seq_id), ":" stands for the whole chain
    "annotations": {                          # pdb-style residue range (auth_seq_id), ":" stands for the whole chain
        "1tqn": {
            "1tqnA": {
                "pdb": "1tqn",
                "chain_id": "A",
                "ranges": ":",
                "auth_chain_id": "A",
                "auth_ranges": ":",
                "uniprot_id": "P08684",
                "uniprot_name": "CP3A4_HUMAN",
                "domain_mappings": [
                    {
                        "domain": "1tqnA00",
                        "source": "CATH",
                        "family": "1.10.630.10",
                        "pdb": "1tqn",
                        "chain_id": "A",
                        "ranges": "7:478"
                    },
                    {
                        "domain": null,
                        "source": "Pfam",
                        "family": "PF00067",
                        "pdb": "1tqn",
                        "chain_id": "A",
                        "ranges": "17:472"
                    }
                ],
                "secondary_structure_elements": [
                    {
                        "label": "A'",
                        "chain_id": "A",
                        "start": 29,
                        "end": 32,
                        "auth_chain_id": "A",
                        "auth_start": 50,
                        "auth_start_ins_code": "",
                        "auth_end": 53,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s121",
                        "metric_value": 8.54,
                        "confidence": "high",
                        "sequence": "ILSY"
                    },
                    {
                        "label": "A",
                        "chain_id": "A",
                        "start": 36,
                        "end": 47,
                        "auth_chain_id": "A",
                        "auth_start": 57,
                        "auth_start_ins_code": "",
                        "auth_end": 68,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s143",
                        "metric_value": 2.98,
                        "confidence": "high",
                        "sequence": "FCMFDMECHKKY"
                    },
                    {
                        "label": "B",
                        "chain_id": "A",
                        "start": 66,
                        "end": 76,
                        "auth_chain_id": "A",
                        "auth_start": 87,
                        "auth_start_ins_code": "",
                        "auth_end": 97,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s208",
                        "metric_value": 3.83,
                        "confidence": "high",
                        "sequence": "PDMIKTVLVKE"
                    },
                    {
                        "label": "B'",
                        "chain_id": "A",
                        "start": 91,
                        "end": 95,
                        "auth_chain_id": "A",
                        "auth_start": 112,
                        "auth_start_ins_code": "",
                        "auth_end": 116,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s251",
                        "metric_value": 16.26,
                        "confidence": "medium",
                        "sequence": "GFMKS"
                    },
                    {
                        "label": "C",
                        "chain_id": "A",
                        "start": 102,
                        "end": 116,
                        "auth_chain_id": "A",
                        "auth_start": 123,
                        "auth_start_ins_code": "",
                        "auth_end": 137,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s294",
                        "metric_value": 1.67,
                        "confidence": "high",
                        "sequence": "DEEWKRLRSLLSPTF"
                    },
                    {
                        "label": "D",
                        "chain_id": "A",
                        "start": 118,
                        "end": 145,
                        "auth_chain_id": "A",
                        "auth_start": 139,
                        "auth_start_ins_code": "",
                        "auth_end": 166,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s316",
                        "metric_value": 13.92,
                        "confidence": "medium",
                        "sequence": "SGKLKEMVPIIAQYGDVLVRNLRREAET"
                    },
                    {
                        "label": "E",
                        "chain_id": "A",
                        "start": 151,
                        "end": 167,
                        "auth_chain_id": "A",
                        "auth_start": 172,
                        "auth_start_ins_code": "",
                        "auth_end": 188,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s359",
                        "metric_value": 2.49,
                        "confidence": "high",
                        "sequence": "LKDVFGAYSMDVITSTS"
                    },
                    {
                        "label": "F",
                        "chain_id": "A",
                        "start": 181,
                        "end": 189,
                        "auth_chain_id": "A",
                        "auth_start": 202,
                        "auth_start_ins_code": "",
                        "auth_end": 210,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s381",
                        "metric_value": 17.99,
                        "confidence": "medium",
                        "sequence": "PFVENTKKL"
                    },
                    {
                        "label": "F'",
                        "chain_id": "A",
                        "start": 197,
                        "end": 205,
                        "auth_chain_id": "A",
                        "auth_start": 218,
                        "auth_start_ins_code": "",
                        "auth_end": 226,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s402",
                        "metric_value": 3.86,
                        "confidence": "high",
                        "sequence": "PFFLSITVF"
                    },
                    {
                        "label": "G'",
                        "chain_id": "A",
                        "start": 206,
                        "end": 215,
                        "auth_chain_id": "A",
                        "auth_start": 227,
                        "auth_start_ins_code": "",
                        "auth_end": 236,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s424",
                        "metric_value": 13.51,
                        "confidence": "medium",
                        "sequence": "PFLIPILEVL"
                    },
                    {
                        "label": "G",
                        "chain_id": "A",
                        "start": 222,
                        "end": 242,
                        "auth_chain_id": "A",
                        "auth_start": 243,
                        "auth_start_ins_code": "",
                        "auth_end": 263,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s445",
                        "metric_value": 15.71,
                        "confidence": "medium",
                        "sequence": "REVTNFLRKSVKRMKESRLED"
                    },
                    {
                        "label": "H",
                        "chain_id": "A",
                        "start": 250,
                        "end": 259,
                        "auth_chain_id": "A",
                        "auth_start": 271,
                        "auth_start_ins_code": "",
                        "auth_end": 280,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s467",
                        "metric_value": 6.91,
                        "confidence": "high",
                        "sequence": "FLQLMIDSQN"
                    },
                    {
                        "label": "I",
                        "chain_id": "A",
                        "start": 271,
                        "end": 303,
                        "auth_chain_id": "A",
                        "auth_start": 292,
                        "auth_start_ins_code": "",
                        "auth_end": 324,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s532",
                        "metric_value": 1.54,
                        "confidence": "high",
                        "sequence": "DLELVAQSIIFIFAGYETTSSVLSFIMYELATH"
                    },
                    {
                        "label": "J",
                        "chain_id": "A",
                        "start": 304,
                        "end": 318,
                        "auth_chain_id": "A",
                        "auth_start": 325,
                        "auth_start_ins_code": "",
                        "auth_end": 339,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s554",
                        "metric_value": 1.52,
                        "confidence": "high",
                        "sequence": "PDVQQKLQEEIDAVL"
                    },
                    {
                        "label": "J'",
                        "chain_id": "A",
                        "start": 326,
                        "end": 331,
                        "auth_chain_id": "A",
                        "auth_start": 347,
                        "auth_start_ins_code": "",
                        "auth_end": 352,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s575",
                        "metric_value": 5.71,
                        "confidence": "high",
                        "sequence": "YDTVLQ"
                    },
                    {
                        "label": "K",
                        "chain_id": "A",
                        "start": 333,
                        "end": 346,
                        "auth_chain_id": "A",
                        "auth_start": 354,
                        "auth_start_ins_code": "",
                        "auth_end": 367,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s597",
                        "metric_value": 1.55,
                        "confidence": "high",
                        "sequence": "EYLDMVVNETLRLF"
                    },
                    {
                        "label": "K'",
                        "chain_id": "A",
                        "start": 377,
                        "end": 382,
                        "auth_chain_id": "A",
                        "auth_start": 398,
                        "auth_start_ins_code": "",
                        "auth_end": 403,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s727",
                        "metric_value": 2.0,
                        "confidence": "high",
                        "sequence": "SYALHR"
                    },
                    {
                        "label": "K''",
                        "chain_id": "A",
                        "start": 395,
                        "end": 398,
                        "auth_chain_id": "A",
                        "auth_start": 416,
                        "auth_start_ins_code": "",
                        "auth_end": 419,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s748",
                        "metric_value": 1.79,
                        "confidence": "high",
                        "sequence": "PERF"
                    },
                    {
                        "label": "L",
                        "chain_id": "A",
                        "start": 424,
                        "end": 441,
                        "auth_chain_id": "A",
                        "auth_start": 445,
                        "auth_start_ins_code": "",
                        "auth_end": 462,
                        "auth_end_ins_code": "",
                        "type": "h",
                        "color": "s770",
                        "metric_value": 0.78,
                        "confidence": "high",
                        "sequence": "MRFALMNMKLALIRVLQN"
                    },
                    {
                        "label": "1-1",
                        "chain_id": "A",
                        "start": 50,
                        "end": 55,
                        "auth_chain_id": "A",
                        "auth_start": 71,
                        "auth_start_ins_code": "",
                        "auth_end": 76,
                        "auth_end_ins_code": "",
                        "type": "e",
                        "color": "s164",
                        "metric_value": 2.5,
                        "confidence": "high",
                        "sequence": "VWGFYD"
                    },
                    {
                        "label": "1-2",
                        "chain_id": "A",
                        "start": 58,
                        "end": 63,
                        "auth_chain_id": "A",
                        "auth_start": 79,
                        "auth_start_ins_code": "",
                        "auth_end": 84,
                        "auth_end_ins_code": "",
                        "type": "e",
                        "color": "s186",
                        "metric_value": 2.03,
                        "confidence": "high",
                        "sequence": "QPVLAI"
                    },
                    {
                        "label": "1-5",
                        "chain_id": "A",
                        "start": 83,
                        "end": 83,
                        "auth_chain_id": "A",
                        "auth_start": 104,
                        "auth_start_ins_code": "",
                        "auth_end": 104,
                        "auth_end_ins_code": "",
                        "type": "e",
                        "color": "s229",
                        "metric_value": 5.55,
                        "confidence": "high",
                        "sequence": "N"
                    },
                    {
                        "label": "3-1",
                        "chain_id": "A",
                        "start": 149,
                        "end": 150,
                        "auth_chain_id": "A",
                        "auth_start": 170,
                        "auth_start_ins_code": "",
                        "auth_end": 171,
                        "auth_end_ins_code": "",
                        "type": "e",
                        "color": "s337",
                        "metric_value": 6.76,
                        "confidence": "high",
                        "sequence": "VT"
                    },
                    {
                        "label": "1-4",
                        "chain_id": "A",
                        "start": 352,
                        "end": 355,
                        "auth_chain_id": "A",
                        "auth_start": 373,
                        "auth_start_ins_code": "",
                        "auth_end": 376,
                        "auth_end_ins_code": "",
                        "type": "e",
                        "color": "s640",
                        "metric_value": 10.06,
                        "confidence": "medium",
                        "sequence": "LERV"
                    },
                    {
                        "label": "2-1",
                        "chain_id": "A",
                        "start": 360,
                        "end": 362,
                        "auth_chain_id": "A",
                        "auth_start": 381,
                        "auth_start_ins_code": "",
                        "auth_end": 383,
                        "auth_end_ins_code": "",
                        "type": "e",
                        "color": "s662",
                        "metric_value": 2.42,
                        "confidence": "high",
                        "sequence": "VEI"
                    },
                    {
                        "label": "2-2",
                        "chain_id": "A",
                        "start": 365,
                        "end": 367,
                        "auth_chain_id": "A",
                        "auth_start": 386,
                        "auth_start_ins_code": "",
                        "auth_end": 388,
                        "auth_end_ins_code": "",
                        "type": "e",
                        "color": "s683",
                        "metric_value": 3.0,
                        "confidence": "high",
                        "sequence": "MFI"
                    },
                    {
                        "label": "1-3",
                        "chain_id": "A",
                        "start": 372,
                        "end": 375,
                        "auth_chain_id": "A",
                        "auth_start": 393,
                        "auth_start_ins_code": "",
                        "auth_end": 396,
                        "auth_end_ins_code": "",
                        "type": "e",
                        "color": "s705",
                        "metric_value": 1.95,
                        "confidence": "high",
                        "sequence": "VVMI"
                    },
                    {
                        "label": "3-3",
                        "chain_id": "A",
                        "start": 442,
                        "end": 445,
                        "auth_chain_id": "A",
                        "auth_start": 463,
                        "auth_start_ins_code": "",
                        "auth_end": 466,
                        "auth_end_ins_code": "",
                        "type": "e",
                        "color": "s791",
                        "metric_value": 1.6,
                        "confidence": "high",
                        "sequence": "FSFK"
                    },
                    {
                        "label": "4-1",
                        "chain_id": "A",
                        "start": 456,
                        "end": 456,
                        "auth_chain_id": "A",
                        "auth_start": 477,
                        "auth_start_ins_code": "",
                        "auth_end": 477,
                        "auth_end_ins_code": "",
                        "type": "e",
                        "color": "s835",
                        "metric_value": 12.71,
                        "confidence": "medium",
                        "sequence": "L"
                    },
                    {
                        "label": "4-2",
                        "chain_id": "A",
                        "start": 464,
                        "end": 464,
                        "auth_chain_id": "A",
                        "auth_start": 485,
                        "auth_start_ins_code": "",
                        "auth_end": 485,
                        "auth_end_ins_code": "",
                        "type": "e",
                        "color": "s878",
                        "metric_value": 9.03,
                        "confidence": "high",
                        "sequence": "P"
                    },
                    {
                        "label": "3-2",
                        "chain_id": "A",
                        "start": 469,
                        "end": 474,
                        "auth_chain_id": "A",
                        "auth_start": 490,
                        "auth_start_ins_code": "",
                        "auth_end": 495,
                        "auth_end_ins_code": "",
                        "type": "e",
                        "color": "s900",
                        "metric_value": 6.31,
                        "confidence": "high",
                        "sequence": "VLKVES"
                    }
                ],
                "beta_connectivity": [
                    [
                        "1-1",
                        "1-2",
                        -1
                    ],
                    [
                        "1-2",
                        "1-3",
                        1
                    ],
                    [
                        "1-5",
                        "1-4",
                        -1
                    ],
                    [
                        "3-1",
                        "3-2",
                        -1
                    ],
                    [
                        "1-4",
                        "1-3",
                        -1
                    ],
                    [
                        "2-1",
                        "2-2",
                        -1
                    ],
                    [
                        "3-3",
                        "3-2",
                        -1
                    ],
                    [
                        "4-1",
                        "4-2",
                        -1
                    ]
                ],
                "rotation_matrix": [
                    0.0841438366722304,
                    -0.9907657680912565,
                    -0.10631560341088532,
                    -0.46321294579603234,
                    0.04653041207831938,
                    -0.10267083975128484,
                    0.99362649895048,
                    -0.12159261906614163,
                    -0.995366633709358,
                    -0.08855445467795255,
                    0.03746162109134595,
                    0.05273612685656731,
                    18.78404164503984,
                    23.992462979534775,
                    13.616655034021722,
                    1.0
                ],
                "comment": "Automatic annotation for 1tqn based on 2NNJ template. Program was called with these parameters: /home/adam/Workspace/C#/SecStrAnnot2_data/SecStrAPI/CytochromesP450-20200128/structures 2NNJ,A,: 1tqn,A,: --soft --label2auth --maxmetric 25,0.5,0.5 --verbose  Total value of used metric: 186.50"
            }
        }
    }
}

</source>

<br style="clear:both" />
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[[SecStrAnnotator:UserManual | Back to the main page]]