SecStrAnnotator:SecStrAPI

Example of using SecStrAPI plugin in PyMOL:
> run https://webchem.ncbr.muni.cz/API/SecStr/Downloads/secstrapi_plugin.py
> annotate_sec_str 1tqn

The SecStrAPI allows programmatic access to precomputed secondary structure annotations. The annotations from SecStrAPI can also be easily visualized in PyMOL using SecStrAPI Plugin.

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 and explained below.

{
    "api_version": "1.0",                           
    "annotations": {
        "1tqn": {                                   # PDB ID
            "1tqnA": {                              # domain ID (unique domain identifier in SecStrAPI)
                "pdb": "1tqn",                      # PDB ID
                "chain_id": "A",                    # mmcif-style chain identifier (label_asym_id)
                "ranges": ":",                      # mmcif-style residue range (label_seq_id), : stands for the whole chain
                "auth_chain_id": "A",               # pdb-style chain identifier (auth_asym_id)
                "auth_ranges": ":",                 # pdb-style residue range (auth_seq_id), : stands for the whole chain
                "uniprot_id": "P08684",             # UniProt accession number
                "uniprot_name": "CP3A4_HUMAN",      # UniProt mnemonic identifier
                "domain_mappings": [                # list of mappings to source databases
                    {
                        "domain": "1tqnA00",        # domain ID in the source database, if available
                        "source": "CATH",           # name of source database
                        "family": "1.10.630.10",    # family ID in the source database
                        "pdb": "1tqn",              # PDB ID
                        "chain_id": "A",            # mmcif-style chain identifier (label_asym_id) of the domain in the source database
                        "ranges": "7:478"           # mmcif-style residue range (label_seq_id) of the domain in the source database (including the number before and after the colon)
                    },
                    {
                        "domain": null,
                        "source": "Pfam",
                        "family": "PF00067",
                        "pdb": "1tqn",
                        "chain_id": "A",
                        "ranges": "17:472"
                    }
                ],
                "secondary_structure_elements": [   # list of annotated secondary structure elements (SSEs)
                    {
                        "label": "1-1",             # SSE label
                        "chain_id": "A",            # mmcif-style chain identifier (label_asym_id)
                        "start": 50,                # mmcif-style residue number of the first residue (label_seq_id)
                        "end": 55,                  # mmcif-style residue number of the last residue (label_seq_id)
                        "auth_chain_id": "A",       # pdb-style chain identifier (auth_asym_id)
                        "auth_start": 71,           # pdb-style residue number of the first residue (auth_seq_id)
                        "auth_start_ins_code": "",  # residue insertion code of the first residue (pdbx_PDB_ins_code)
                        "auth_end": 76,             # pdb-style residue number of the last residue (auth_seq_id)
                        "auth_end_ins_code": "",    # residue insertion code of the last residue (pdbx_PDB_ins_code)
                        "type": "e",                # SSE type (h: helix, e: beta-strand)
                        "sheet_id": 1,              # beta-sheet identifier (all strands in the same sheet have the same sheet_id)
                        "color": "s164",            # pymol-style color assigned to this SSE (consistent through the whole family)
                        "metric_value": 2.5,        # measure of deviation from the template
                        "confidence": "high",       # confidence of the annotation (high: metric_value <= 10, medium: 10 < metric_value <= 20, low: metric_value > 20)
                        "sequence": "VWGFYD"        # amino acid sequence of the SSE
                    },
                    {
                        "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",
                        "sheet_id": 1,
                        "color": "s186",
                        "metric_value": 2.03,
                        "confidence": "high",
                        "sequence": "QPVLAI"
                    },
                    {
                        "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"
                    }
                ],
                "beta_connectivity": [              # list of connections between strands in beta-sheets
                    [
                        "1-1",                      # label of the first strand
                        "1-2",                      # label of the second strand
                        -1                          # relative orientation of the strands (1: parallel, -1: antiparallel)
                    ]
                ],
                "rotation_matrix": [                # PyMOL object matrix used to align the domain to the template
                    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"
            }
        }
    }
}

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