SecStrAnnotator:SecStrAPI
The SecStrAPI allows programmatic access to precomputed secondary structure annotations.
Requests
-
The annotation for a particular PDB entry is accessible by:
https://webchem.ncbr.muni.cz/API/SecStr/Annotation/{pdbid}
Example:https://webchem.ncbr.muni.cz/API/SecStr/Annotation/1tqn -
The list of available PDB entries and the annotated domains in each entry is accessible by:
https://webchem.ncbr.muni.cz/API/SecStr/List/Annotation
SecStrAPI format
The annotations are provided in SecStrAPI JSON format, demonstrated below.
{
"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"
}
}
}
}