Zhanglab forum

To differentiate different ligands of the same type in the same chain, the tsv file offers at column 7 the Ligand serial number. For example, PDB 117e chain A (https://zhanggroup.org/BioLiP/qsearch.c ... 7e&chain=A) has three MN and two PO4. The first 7 columns of the corresponding tsv reads: 11...

One single ligand in a single structure could bind two or more different chains (with different or identical uniprot ID). For example, the first ATP in chain A of 7f04 simultaneously binds protein chain A and chain E: https://zhanggroup.org/BioLiP2/pdb.cgi?pdb=7f04&chain=A&bs=BS02 https://zh...

This is not a bug. BioLiP.txt.gz list all ~816 K protein-ligand interactions. A ligand may interact with one or more proteins. The number of unique ligands at https://zhanggroup.org/BioLiP/weekly.html is smaller, at ~585 K.

We have fixed the issue for 8gwo:G. The webpage you mention should now work. u0 is not a mistake. If you check line 22085 to line 22104 of the PDB format file for 8gwo at https://files.rcsb.org/view/8GWO.pdb, you will notice that residue 0 of chain G is ribonucleotide U, while the remaining residues...

I test US-align on your model and do not observe any issue: curl "https://zhanggroup.org/forum/download/file.php?id=60&sid=e7d55819c30ec4ed7cf974e16cdc5b4e" -o dino_models.zip unzip dino_models.zip USalign -dir dino_models/ dino_models/input_list -suffix .pdb -mm 4 ********************...

You issue may be related to https://github.com/pylelab/USalign/issu ... 1356474145 where your pdb file does not have standard atom name. Please check if this is the case.

Can you attach the content of "dino_models/" as a zip archive in your next post so that we can check what the issue is?

We do not have programs to predict DNA structure. Sorry.

Unfortunately, your job was not correctly parsed by our server due to internal bug. I have already resubmitted your protein as job T11532. If you did not receive result by next week, please let us know.

This is an issue related to the EMrefinement.pl script of I-TASSER. Could you send us the closc*pdb, combo*pdb and model*pdb files of your job as a zip file? We can further check what the issue is.