Search found 71 matches
- Thu Mar 09, 2023 12:41 am
- Forum: Main Forum
- Topic: Ligand Serial Number
- Replies: 9
- Views: 36265
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...
- Sat Feb 11, 2023 2:02 pm
- Forum: Main Forum
- Topic: BioLiP inquiry
- Replies: 5
- Views: 20613
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...
- Fri Feb 10, 2023 8:41 pm
- Forum: Main Forum
- Topic: BioLiP inquiry
- Replies: 5
- Views: 20613
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.
- 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: 16862
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...
- Tue Dec 20, 2022 7:29 pm
- Forum: Main Forum
- Topic: MSTA issue
- Replies: 5
- Views: 12998
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 ********************...
- Sat Dec 17, 2022 9:18 pm
- Forum: Main Forum
- Topic: MSTA issue
- Replies: 5
- Views: 12998
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.
- Sat Dec 17, 2022 2:06 pm
- Forum: Main Forum
- Topic: MSTA issue
- Replies: 5
- Views: 12998
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?
- Tue Jul 05, 2022 4:07 pm
- Forum: Main Forum
- Topic: 3D Structure of Methylated DNA
- Replies: 1
- Views: 3759
Re: 3D Structure of Methylated DNA
We do not have programs to predict DNA structure. Sorry.
- Thu Jun 23, 2022 8:46 pm
- Forum: Main Forum
- Topic: ThreaDom Processing (Job T11532)
- Replies: 4
- Views: 6420
Re: ThreaDom Processing (Job T11532)
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.
- Fri Jun 03, 2022 6:22 pm
- Forum: Main Forum
- Topic: Error in final PDB model generated by I-TASSER standalone program
- Replies: 2
- Views: 3537
Re: Error in final PDB model generated by I-TASSER standalone program
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.