Search found 74 matches

by zcx@umich.edu
Wed Mar 15, 2023 6:53 pm
Forum: Main Forum
Topic: Ligand Serial Number
Replies: 9
Views: 38552

Re: Ligand Serial Number

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...
by zcx@umich.edu
Fri Mar 10, 2023 7:43 pm
Forum: Main Forum
Topic: Ligand Serial Number
Replies: 9
Views: 38552

Re: Ligand Serial Number

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 ...
by zcx@umich.edu
Thu Mar 09, 2023 6:21 pm
Forum: Main Forum
Topic: Query to maximum input in PEPPI
Replies: 1
Views: 14197

Re: Query to maximum input in PEPPI

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.
by zcx@umich.edu
Thu Mar 09, 2023 12:41 am
Forum: Main Forum
Topic: Ligand Serial Number
Replies: 9
Views: 38552

Re: Ligand Serial Number

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...
by zcx@umich.edu
Sat Feb 11, 2023 2:02 pm
Forum: Main Forum
Topic: BioLiP inquiry
Replies: 5
Views: 21727

Re: BioLiP inquiry

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...
by zcx@umich.edu
Fri Feb 10, 2023 8:41 pm
Forum: Main Forum
Topic: BioLiP inquiry
Replies: 5
Views: 21727

Re: BioLiP inquiry

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.
by zcx@umich.edu
Fri Feb 03, 2023 5:34 pm
Forum: Main Forum
Topic: crash on biolip web site and a site at position 0
Replies: 2
Views: 17826

Re: crash on biolip web site and a site at position 0

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...
by zcx@umich.edu
Tue Dec 20, 2022 7:29 pm
Forum: Main Forum
Topic: MSTA issue
Replies: 5
Views: 14237

Re: MSTA issue

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 ********************...
by zcx@umich.edu
Sat Dec 17, 2022 9:18 pm
Forum: Main Forum
Topic: MSTA issue
Replies: 5
Views: 14237

Re: MSTA issue

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.
by zcx@umich.edu
Sat Dec 17, 2022 2:06 pm
Forum: Main Forum
Topic: MSTA issue
Replies: 5
Views: 14237

Re: MSTA issue

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?