Zhanglab forum

Ok, good to know.

I noticed that the BioLiP database has 420307 ligand entries now, as compared to 454406 on July 20 (https://web.archive.org/web/20230720112 ... /index.cgi). Were some entries removed?

Is there some documentation of what these two columns in the bio lip tsv mean? My guess is that ligand chain is the pdb chain that the ligand is located on and receptor chain is the chain that the binding site residues are located on--is that correct? I realize there is a README file, but it doesn't...

Hi,
Following up on this, it looks like some of the ligand residue numbers have letters in them e.g. 479G.

Wow, thank you! That's very helpful and will save you a lot of API requests.

I actually need access to the atoms of the bound ligand within the pdb file, rather than just a separate file containing just the ligand. Is there a way to do that?

Thanks for the response! However, I'm still confused. I understand that the Ligand Serial Number can tell us the "index" of the ligand in the mmCIF file for that chain, ie Ligand Serial Number 2 would mean it's the second ligand mentioned in that chain with that name. I'm still confused ho...

How is the Ligand Serial Number column created? I want to be able to extract the bound ligand from the pdb structure based on the information available in the BioLip TSV. I know I can download the ligand from BioLip as well but I'd prefer not to have to download additional structures if possible. If...