Clarification question about BioLip database

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akabir
Posts: 3
Joined: Thu Sep 29, 2022 2:42 pm

Clarification question about BioLip database

Post by akabir »

I have some quick clarification question about BioLip database.

1. The items in "BioLiP in numbers" section in this link says, "Number of DNA/RNA ligands: 60,539". I think this indicates "Number of entries that binds to DNA/RNA ligands: 60,539"?
2. Is there any way to separate the entries for DNA binding and RNA binding?
3. Is there any way that I can download only those entries corresponding to DNA and/or RNA (or only metal or only protein or only regular/small ligand) ligands?
4. Ligand Id "NUC" and "III" stands for DNA/RNA ligands and peptide ligands, respectively. Is there any document/link that gives the ligand ids for metal and regular ligands?
jlspzw
Posts: 94
Joined: Tue May 04, 2021 5:04 pm

Re: Clarification question about BioLip database

Post by jlspzw »

Dear user,

For 1, Yes, you are correct
For 2, You may first download the entire BioLip and count them separately
For 3, Unfortunately, you can only download the entire BioLip, which actually is not that large.
For 4, Ligand ID: This can be the standard 3-letter code of ligand from PDB and MMCIF files. you can either download the entire BioLip and find the ligand name in it or goto PDB to find the instruction of the 3-letters code http://ligand-expo.rcsb.org/ld-download.html. However, based on my known, it seems there is no separate database that only records the metal-ligand.

Best
IT team
akabir
Posts: 3
Joined: Thu Sep 29, 2022 2:42 pm

Re: Clarification question about BioLip database

Post by akabir »

Thanks a lot.
Followup on 2: I see LigandID==NUC indicates all the DNA/RNA ligand binding entries. Then, how can I separate them?
jlspzw
Posts: 94
Joined: Tue May 04, 2021 5:04 pm

Re: Clarification question about BioLip database

Post by jlspzw »

Dear user,

Unfortunately, we didn't separate the RNA and DNA. But after you download the BioLip, you can find the pdb id for each entry. First, check the ligand ID NUC, then go to PDB and download the pdb/fasta based on pdb id for each entry. check the NUC ligand sequence. If the sequence contains 'U', then it should be RNA, otherwise, it is DNA.

Best
IT team
akabir
Posts: 3
Joined: Thu Sep 29, 2022 2:42 pm

Re: Clarification question about BioLip database

Post by akabir »

You are absolutely right. That makes sense. Thanks.
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