How to compute LDDT (Prot-Prot, Lig-Prot....)

[chensiyuan030105]

ould you please explain how to compute the other LDDT metrics (Prot-Prot, Lig-Prot, DNA-Prot, RNA-Prot, Intra-Prot, Mean LDDT-PLI) besides Complex LDDT?

[cloverzizi]

Hi @chensiyuan030105 ,

After running PXMeter, the LDDT values for all chains and interfaces are included in the output JSON. For example:

...
"complex": {
        "clashes": 0,
        "lddt": 0.9469227849197736
    },
    "chain": {
        "A": {
            "lddt": 0.9589892443592952
        },
        "B": {
            "lddt": 0.9442877198559017
        },
        "C": {
            "lddt": 0.9349607075816869
        }
    },
    "interface": {
        "A,B": {
            "lddt": 0.9218669898327078,
...

Here, the Chain ID corresponds to the Chain ID in the reference.
In the "ref_chain_info" field of the JSON, each chain is annotated with its corresponding "entity_type":

"ref_chain_info": {
        "A": {
            "label_entity_id": "1",
            "entity_type": "polypeptide(L)"
        },
        "B": {
            "label_entity_id": "2",
            "entity_type": "polydeoxyribonucleotide"
        },
        "C": {
            "label_entity_id": "3",
            "entity_type": "polydeoxyribonucleotide"
        }
    }

The typical "entity_type" values are:

• polypeptide(L) – Protein
• polydeoxyribonucleotide – DNA
• polyribonucleotide – RNA
• ligand – Ligand

For example, if the "lddt" value of chain A in the JSON is 0.946, and its "entity_type" is "polypeptide(L)", then the Intra-Prot metric for chain A is 0.946.