Zhanglab forum

Yes, we do provide the reference ID, including chembl id, IUPAC name, smiles, inchi and inchi key at https://zhanggroup.org/GLASS/downloads/ligands.tsv No, we cannot combine ligands.tsv and the interaction data in one file. One ligand can bind to multiple different GPCRs. If we try to combine the tw...

Both of your two submitted jobs has been completed on March 27. They are available at
https://zhanggroup.org/I-TASSER/output/S729416/maxh6t/
https://zhanggroup.org/I-TASSER/output/S729513/u8aj5g/

Your job should have been completed at https://zhanggroup.org/COTH/output/S3973A-S3973B/

This is not a bug. Some ligand residue numbers have insertion code (https://proteopedia.org/wiki/index.php/ ... tion_Codes). In your example, 479G means the ligand is residue 419 with insertion code G.

USalign only reads atoms of interest. For example, for RNA, US-align by default only reads C3', completely ignoring other atoms and non-ATOM lines. This makes impossible for US-align to differentiate if the file does not have atom at all or just not have C3'. This is for efficiency purpose. Why it i...

If you click "Download" to download the ligand sdf file, you will get the ligand 3d structure. You can also use a text editor to open the ligand sdf file to get information such as smiles string, molecular weight etc.

The bug for BioLiP link should have been fixed by now.

DeepMSA2 is currently under review. We will release the standalone version once the manuscript is accepted.

As per your request, I have updated the tsv file to include the residue sequence number as the last but one column in BioLiP.txt.

I have updated the tsv file to include the residue sequence number as the last but one column in BioLiP.txt.