Search found 157 matches
- Sat Jan 08, 2022 12:51 am
- Forum: Main Forum
- Topic: Not able to run previous protein modelled structure
- Replies: 1
- Views: 2081
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!
- Tue Dec 21, 2021 11:46 am
- Forum: Main Forum
- Topic: Downloading D-I-Tasser Suite
- Replies: 3
- Views: 2855
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.
- Tue Dec 21, 2021 11:43 am
- Forum: Main Forum
- Topic: Building a 3D model by using specified template
- Replies: 1
- Views: 2057
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.
- Thu Dec 16, 2021 7:25 am
- Forum: Main Forum
- Topic: LSalign | Transformation Bug
- Replies: 2
- Views: 3118
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...
- Tue Dec 14, 2021 1:01 pm
- Forum: Main Forum
- Topic: issues with docking result
- Replies: 1
- Views: 9115
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...
- Tue Dec 14, 2021 2:50 am
- Forum: Main Forum
- Topic: Forcing a template to build a missing piece...
- Replies: 1
- Views: 2071
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.
- Mon Dec 13, 2021 1:25 am
- Forum: Main Forum
- Topic: ligand preparation + binding energies and VDW/HB scores
- Replies: 1
- Views: 2269
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.
- Sun Dec 12, 2021 9:42 pm
- Forum: Main Forum
- Topic: question about SPRING score
- Replies: 1
- Views: 2256
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.
- Thu Dec 09, 2021 9:07 pm
- Forum: Main Forum
- Topic: Issue with MM-align on-line
- Replies: 1
- Views: 2010
Re: Issue with MM-align on-line
You can download the standalone package and run it locally. Here is my result. Please let me know if you have any questions.
- Thu Dec 09, 2021 8:03 pm
- Forum: Main Forum
- Topic: Output files from EDTSurf
- Replies: 1
- Views: 1913
Re: Output files from EDTSurf
Please use the option "-s 0" to generated the ".dep" files. Please let me know if you have any questions.