Zhanglab forum

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.

I have just updated the BioLiP web interface to add the residue information. For example, at https://zhanggroup.org/BioLiP2/pdb.cgi?pdb=8gwo&chain=G&bs=BS01 the "Ligand information" says "8gwo Chain A Residue 1003" where 1003 is the residue sequence number (_atom_site.aut...

If your purpose is to load the structure of the ligand, you can directly batch download all ligand structure from https://zhanggroup.org/BioLiP/weekly.html If you only need one specific ligand in a structure of your interest, you can download it from the "[Download ligand structure]" link ...

If you have to handle longer sequence, you will need to download and install PEPPI from https://github.com/ewbell94/PEPPI and run it on your own computer.