Search found 139 matches

by xiaogenz
Sat Jan 08, 2022 1:01 am
Forum: Main Forum
Topic: COFACTOR Query (Delayed?)
Replies: 9
Views: 1681

Re: COFACTOR Query (Delayed?)

Sorry! Our computer cluster is not stable now, while our system admin is still on vacation. We will solve the problem as soon as possible.
by xiaogenz
Sat Jan 08, 2022 12:57 am
Forum: Main Forum
Topic: COTH Input Query
Replies: 2
Views: 709

Re: COTH Input Query

Sorry! The COTH server currently cannot upload templates. You may try to use I-TASSER to build the monomer models, and then input the HDOCK server (http://hdock.phys.hust.edu.cn/) for docking.
by xiaogenz
Sat Jan 08, 2022 12:51 am
Forum: Main Forum
Topic: Not able to run previous protein modelled structure
Replies: 1
Views: 562

Re: Not able to run previous protein modelled structure

What's your job ID or your email address? We will check it for you. Thank you!
by xiaogenz
Tue Dec 21, 2021 11:46 am
Forum: Main Forum
Topic: Downloading D-I-Tasser Suite
Replies: 3
Views: 867

Re: Downloading D-I-Tasser Suite

Sorry! The D-I-TASSER suite is not available for public download now. We are still packing the program and we will make it public when complete.
by xiaogenz
Tue Dec 21, 2021 11:43 am
Forum: Main Forum
Topic: Building a 3D model by using specified template
Replies: 1
Views: 601

Re: Building a 3D model by using specified template

You can use the Option I of the I-TASSER server to provide your template to guide the modeling. The template with alignment is recommended. Please let me know if you have any questions when you use the option.
by xiaogenz
Thu Dec 16, 2021 7:25 am
Forum: Main Forum
Topic: LSalign | Transformation Bug
Replies: 2
Views: 793

Re: LSalign | Transformation Bug

The error is caused by the file format required by LSalign. I have converted the format of the input model (see attachment) using OpenBabel and the program is working now. Here is the result: https://zhanggroup.org/LS-align/output/LS1639630900_621874/ Please let me know if you have any questions. 51...
by xiaogenz
Tue Dec 14, 2021 1:01 pm
Forum: Main Forum
Topic: issues with docking result
Replies: 1
Views: 603

Re: issues with docking result

It is possible to obtain different docking poses for the same receptor and ligand when you run several times for docking programs. The initial docking poses are different because the program starts from randomly translating the ligand into the binding pocket, then does simulation to find the docking...
by xiaogenz
Tue Dec 14, 2021 2:50 am
Forum: Main Forum
Topic: Forcing a template to build a missing piece...
Replies: 1
Views: 588

Re: Forcing a template to build a missing piece...

You can try to use our newly developed program DEMO-EM (https://zhanggroup.org/DEMO-EM/) by considering each chain as a virtual domain. Please let us know if you need any help.
by xiaogenz
Mon Dec 13, 2021 1:25 am
Forum: Main Forum
Topic: ligand preparation + binding energies and VDW/HB scores
Replies: 1
Views: 713

Re: ligand preparation + binding energies and VDW/HB scores

Thank you for your questions. The ligand should be adder H atoms because the docking score is related the item. We hope EDock software is helpful for your project.
by xiaogenz
Sun Dec 12, 2021 9:42 pm
Forum: Main Forum
Topic: question about SPRING score
Replies: 1
Views: 713

Re: question about SPRING score

As I understand it, ZscoreA and ZscoreB correspond to ZA and ZB in the equation, respectively. TMscoreA and TMscoreB are used to determine the second term TM which is described in Page 719 of the paper. It seems the file did not report the third term.