Can two slightly different （length）sequence be allplied to DockQ algorithm?

[Ming-Qin-tech]

In Flexible docking cases, a same protein pdbid can have slightly different before and after this flexible docking. For example, If I extract the protein sequence from "1a2k_receptor_unbound.pdb", the chain A's sequence is :"GDKPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMFRLALHNF"

However, the sequence from "1a2k_receptor_bound.pdb" is : "KPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMFRLALHNFG".

we can see the different of the sequence length. To evaluate the felxible docking model performance, I want to run DockQ algprithm to evaluate the two pdb file. The question is: can Can two slightly different （length）sequence be allplied to DockQ algorithm?

[Ming-Qin-tech]

If cannot use it, what strategy your suggested to cut the sequence to maintain the same length? now I am trying sequence align algorithm to cut the longer sequence.

[clami66]

Hi, if I understand correctly your question then yes, DockQ realigns the sequences and only performs comparisons on the parts that are in both the model and the reference structures

[Ming-Qin-tech]

Oh,Thx!