Zhanglab forum

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

"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.

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