What the meaning of "interest ligand"?

[leaves520]

Hi~ @maabuu ,

I recently had the pleasure of reading your publication and I must commend you on the excellent work. The depth of research and the clarity in presenting your findings are truly impressive and have significantly contributed to my understanding of the topic.

However, I encountered a point in the paper that I would appreciate some clarification on. Specifically, I am a bit confused about the term "interest ligand" used in the study. Could you kindly explain how "interest ligand" is defined and identified within the context of your research?

Thank you very much for your time and assistance. I look forward to your response.

Best regards.

[maabuu]

The term "ligand of interest" is adopted from the PDB that uses this label for small molecules that were the subject of the research the structure was generated for. The very last section here explains it: https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/small-molecule-ligands

[leaves520]

Thank you for your timely reply！
So, does this mean that all the ligands in PoseBuster come from the original PDB entries labeled as 'ligand of interest'? Are the remaining (eg. CCD) ones considered cofactors?

[maabuu]

Yes, that is right. Only ligands marked as "ligands of interest" were chosen for the PoseBusters data set. These are removed from the protein complexes and the task is to re-dock them. Water molecules and solvents are also removed but other small molecules were kept in the structures.

[leaves520]

Well，If there are multiple "ligands of interest" in one PDB, how did the PoseBusters choose?

[maabuu]

First, a number of quality filters (Methods section, Table S1) are applied. After the filters, if there were multiple valid ligands per structure, one was selected randomly for the PoseBusters set to have only one ligand per PDB structure.