Readme:./DockQ.py <model> <native>

[Kaixiang-Wang]

I want to predict the docking scores of the result of Alphafold-Multimer by DockQ. However, I have no idea which file is "model" and which one is "native".

[nemo8130]

'model' refers to the docked 'A-B' pose (one wants to assess the quality of) while 'native' is the native 'A-B' complex, solved experimentally. Both files should be in PDB (Brookhaven) format. DockQ assesses the quality of the docked complex compared to its native reference.

[Kaixiang-Wang]

Thank you so much , so that DockQ can not predict the protein-protein docking scores which is not solved by experiment. Am I right?

[nemo8130]

Yes, for that you need a protein-protein docking scoring function (you may try: ProQDock which is a Support Vector Regression Machine trained on high-level structural descriptors and has used DockQ as its target function: https://academic.oup.com/bioinformatics/article/32/12/i262/2288786).

DockQ is instead a 'quality estimate' for protein-protein docked poses for which the experimental structural template is available as a reference.

[Kaixiang-Wang]

Your advice is of great help to me and I will try it as soon as possible.

[nemo8130]

You are welcome. The ProQDock github package is available here: https://github.com/bjornwallner/ProQDock

[Kaixiang-Wang]

When I go to page ProQDock, I find the 'model.pdb' in example file is a two different protein heteromer (two different protein interact) but in the 'fulllength.fasta', there is only one protein sequence. Whether all the heteromer we need to get sequence with 'ProQDock/EXEC/pdb2fasta.pl' or I can input two protein sequence in the same fasta file to the program.

[nemo8130]

For these functionality details please refer to the corresponding author of the paper (Prof. Bjorn Wallner, bjorn.wallner@liu.se) who updates and maintains the package eversince my post doctoral tenure was over in that lab. Though, for this particular query, I believe it is made quite clear in the instructions.

[Kaixiang-Wang]

yes, thank you so much.

[bjornwallner]

The full length is the sequences concatinated.

Björn

On 5 Jan 2022, at 14:13, Kaixiang-Wang @.***> wrote:



When I go to page ProQDock, I find the 'model.pdb' in example file is a two different protein heteromer (two different protein interact) but in the 'fulllength.fasta', there is only one protein sequence. Whether all the heteromer we need to get sequence with 'ProQDock/EXEC/pdb2fasta.pl' or I can input two protein sequence in the same fasta file to the program.

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