Search found 71 matches
- Thu Mar 30, 2023 6:17 pm
- Forum: Main Forum
- Topic: Ligand Serial Number
- Replies: 9
- Views: 36091
Re: Ligand Serial Number
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.
- Mon Mar 27, 2023 4:46 pm
- Forum: Main Forum
- Topic: USalign 的错误提示建议
- Replies: 1
- Views: 13283
Re: USalign 的错误提示建议
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...
- Wed Mar 22, 2023 12:07 pm
- Forum: Main Forum
- Topic: Request for help_COACH
- Replies: 1
- Views: 15357
Re: Request for help_COACH
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.
- Wed Mar 22, 2023 12:58 am
- Forum: Main Forum
- Topic: Link not working
- Replies: 2
- Views: 16419
Re: Link not working
The bug for BioLiP link should have been fixed by now.
- Tue Mar 21, 2023 1:12 pm
- Forum: Main Forum
- Topic: when will deepmsa2 standalone version become available
- Replies: 2
- Views: 22972
Re: when will deepmsa2 standalone version become available
DeepMSA2 is currently under review. We will release the standalone version once the manuscript is accepted.
- Fri Mar 17, 2023 12:54 pm
- Forum: Main Forum
- Topic: BioLiP inquiry
- Replies: 5
- Views: 20503
Re: BioLiP inquiry
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.
- Fri Mar 17, 2023 12:53 pm
- Forum: Main Forum
- Topic: Ligand Serial Number
- Replies: 9
- Views: 36091
Re: Ligand Serial Number
I have updated the tsv file to include the residue sequence number as the last but one column in BioLiP.txt.
- Wed Mar 15, 2023 6:53 pm
- Forum: Main Forum
- Topic: Ligand Serial Number
- Replies: 9
- Views: 36091
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...
- Fri Mar 10, 2023 7:43 pm
- Forum: Main Forum
- Topic: Ligand Serial Number
- Replies: 9
- Views: 36091
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 ...
- Thu Mar 09, 2023 6:21 pm
- Forum: Main Forum
- Topic: Query to maximum input in PEPPI
- Replies: 1
- Views: 13507
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.