output meaning?

[holeung]

Can you please explain the output data? From the example data, I cannot find the output scores of the protein-ligand complex. Are higher scores better? Is there a way to convert to affinity?

[sc8668]

The higher is the better. I'm so sorry that this version cannot convert the score into affinity. This score can just represent the relative binding strengths between two complexes.

[holeung]

Thank you. I still do not understand the meaning of the rest of the output. For example, what is 1qkt_55-9? I assume it is referring to a decoy. Where is the score of the real ligand?

id,score
1qkt_55-9,63.40108607564977
1qkt_714-23,62.08828292760486
1qkt_150-3,60.94627539178022
1qkt_718-24,60.38113679771106

[sc8668]

All of these molecules refer to decoys. If you want to score the real ligand, please replace the input "1qkt_decoys.sdf" with "1qkt_l.sdf" (a file representing the real ligand).

[holeung]

What is the second number after the decoy name? For example, for "1qkt_55-9", what is "9"?

[sc8668]

An index that indicates the order of the ligands in a specific file. If the input file has 10 ligands, the first one is labeled as 0, the second as 1, and so on.