BioLiP coordinates

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drichard
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Joined: Wed Mar 23, 2022 1:47 pm

BioLiP coordinates

Post by drichard »

Hello,
I was interested in using your BioLiP ligand and catalytic site dataset to intersect with some residues of interest I have in some proteins.
However, one question I had was regarding the coordinates of residues in ligand/catalytic sites - the website indicates that the 'Annotation' files have both residues coordinates based on the PDB numbering, as well as coordinates 'renumbered to 1'. When the coordinates are 'renumbered to 1' - does this mean that the residues are aligned with the Uniprot reference protein sequence? For example, if there's an A33 residue in the 'renumbered to 1' coordinates of a site, will this correspond to an A33 residue in the Uniprot reference sequence? Just wondering if I had to map all the coordinates from your sites to the Uniprot sequences.

As well, I had also downloaded the entire BioLip dataset from the 'browse' tab - are these residue coordinates relative to the PDB numbering, or have they also be renumbered to 1?

Thank you for your time,

Daniel Richard
zcx@umich.edu
Posts: 24
Joined: Wed Nov 03, 2021 5:59 pm

Re: BioLiP coordinates

Post by zcx@umich.edu »

"renumbered to 1" means that we reindex residue numbers (column 23-26 of the PDB atomic coordinate http://www.wwpdb.org/documentation/file ... .html#ATOM) such that the first residue is residue 1, the second residue is residue 2 etc.
It is not related to residue number in uniprot.
zcx@umich.edu
Posts: 24
Joined: Wed Nov 03, 2021 5:59 pm

Re: BioLiP coordinates

Post by zcx@umich.edu »

If you need to download BioLiP dataset, you may want to use https://zhanggroup.org/BioLiP/download.html rather than "browse".
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