Search found 69 matches

by zcx@umich.edu
Sun Jun 04, 2023 12:45 am
Forum: Main Forum
Topic: On FASPR and rotamer sampling
Replies: 2
Views: 3311

Re: On FASPR and rotamer sampling

FASPR aims to achieve the global minimum energy configuration (GMEC) by fully deterministic algorithms, such as dead end elimination. Therefore, it is not possible to force it to generate multiple conformation. The temp variable in Search.cpp is not related to temperature annealing.
by zcx@umich.edu
Sun Jun 04, 2023 12:45 am
Forum: Main Forum
Topic: On FASPR and rotamer sampling
Replies: 2
Views: 3311

On FASPR and rotamer sampling

From: <l*@opnbnch.com> Date: Friday, June 2, 2023 at 14:25 Subject: On FASPR and rotamer sampling Hi Prof. Zhang, I've been really impressed with using your FASPR tool - it's very fast and generates plausible coordinates. It's been a great addition to the suite of protein structure modeling tools ou...
by zcx@umich.edu
Thu Jun 01, 2023 4:37 pm
Forum: Main Forum
Topic: Forum Registration Error
Replies: 1
Views: 5366

Re: Forum Registration Error

The message "The solution you provided was incorrect" was caused by the password being too weak, i.e., <6 characters, does not have numbers, or does not have both upper and lower cases. Can you explain how did you get triggers the "Invalid domain for site key" error? This is like...
by zcx@umich.edu
Thu Jun 01, 2023 4:36 pm
Forum: Main Forum
Topic: Forum Registration Error
Replies: 1
Views: 5366

Forum Registration Error

From: <k***@gmail.com> Date: Friday, June 2, 2023 at 00:11 To: Yang Zhang <zhang@zhanggroup.org> Subject: Forum Registration Error Hello, I am receiving errors while attempting to register for the forum and I'm wondering if you could direct me to someone who can assist. The forum help page says to c...
by zcx@umich.edu
Tue Apr 18, 2023 1:27 am
Forum: Main Forum
Topic: Receptor Chain vs Ligand Chain
Replies: 1
Views: 7079

Re: Receptor Chain vs Ligand Chain

Yes, that is correct.
by zcx@umich.edu
Tue Apr 18, 2023 1:26 am
Forum: Main Forum
Topic: REQUIREMENT FOR THE OTHER UNIVERSAL CHEMICAL IDS
Replies: 1
Views: 6689

Re: REQUIREMENT FOR THE OTHER UNIVERSAL CHEMICAL IDS

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...
by zcx@umich.edu
Sun Apr 09, 2023 1:53 am
Forum: Main Forum
Topic: Result from I-TASSER server
Replies: 1
Views: 9372

Re: Result from I-TASSER server

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/
by zcx@umich.edu
Mon Apr 03, 2023 2:21 am
Forum: Main Forum
Topic: Result from COTH server
Replies: 1
Views: 8651

Re: Result from COTH server

Your job should have been completed at https://zhanggroup.org/COTH/output/S3973A-S3973B/
by zcx@umich.edu
Thu Mar 30, 2023 6:17 pm
Forum: Main Forum
Topic: Ligand Serial Number
Replies: 9
Views: 20481

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.
by zcx@umich.edu
Mon Mar 27, 2023 4:46 pm
Forum: Main Forum
Topic: USalign 的错误提示建议
Replies: 1
Views: 6846

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...