Search found 226 matches

by jlspzw
Thu Feb 29, 2024 10:58 pm
Forum: Main Forum
Topic: TM-align results
Replies: 3
Views: 26

Re: TM-align results

Dear user,

Yes, you definitely can use the results for publications, we would appreciate it if you could cite our TM-align work that appears on the website. Thank you.

Best Regards
Wei Zheng
by jlspzw
Wed Feb 28, 2024 12:40 pm
Forum: Main Forum
Topic: Questions about the new version of DMFold
Replies: 1
Views: 44

Re: Questions about the new version of DMFold

Dear Gary, AlphaFold2 default pipeline indeed uses HHsearch to detect the template which will be one of the inputs, so it is correct for modeling. You are also correct if you do not want to use a template, you can set the seqcut parameter as 0, then the template features will be set as NA in the AF2...
by jlspzw
Mon Feb 26, 2024 4:55 am
Forum: Main Forum
Topic: D-I-TASSER Job Running for 13 days
Replies: 3
Views: 85

Re: D-I-TASSER Job Running for 13 days

Dear user,

The issue of your jobs has been fixed, and now it goes into the simulation step. We expect the jobs could be completed in the next 3-5 days. Let us know if you have any other issues or could get the results next week. Thank you for your bug reporting.

Best Regards
Wei Zheng
by jlspzw
Sun Feb 25, 2024 4:07 pm
Forum: Main Forum
Topic: D-I-TASSER Job Running for 13 days
Replies: 3
Views: 85

Re: D-I-TASSER Job Running for 13 days

Dear user,

It is somehow related to our former library issue. But you can let me know the job ids, I will check if any issues with your jobs.

Best Regards
Wei Zheng
by jlspzw
Sun Feb 25, 2024 4:04 pm
Forum: Main Forum
Topic: "DMFAF2 jobs are not complete yet" End in Run_DMFold.py
Replies: 1
Views: 51

Re: "DMFAF2 jobs are not complete yet" End in Run_DMFold.py

Dear Xilong, To speed up the modeling process, we fine-tune the maximal modeling MSA pair as 25 (scoring MSAs by M-score, see the paper for details), thus you get 25*5*5=625 models. The results you get are complete. While, if you want to generate more models, you can enlarge the cutoff from 25 to mo...
by jlspzw
Sat Feb 24, 2024 1:38 pm
Forum: Main Forum
Topic: How to obtain protein complex pdb with DMFold?
Replies: 1
Views: 45

Re: How to obtain protein complex pdb with DMFold?

Dear user,

If you want to get the complex structure, please download the DMFold package instead of DeepMSA2.

https://zhanggroup.org/DMFold/

Best Regards
Wei Zheng
by jlspzw
Fri Feb 23, 2024 4:52 am
Forum: Main Forum
Topic: Multiple sequences
Replies: 1
Views: 67

Re: Multiple sequences

Dear user, We do not accept multiple submissions at one time, and since we have a lot of users and limited resources, to serve more, we limit one job/user. If you want to run more, you can download our standalone package. Let us know if you have any other questions, or if you need any help. Best Reg...
by jlspzw
Fri Feb 23, 2024 4:48 am
Forum: Main Forum
Topic: I-TASSER standalone suite installation
Replies: 7
Views: 105

Re: I-TASSER standalone suite installation

Dear Righteous,

This is the available link https://zhanggroup.org/library/nr.tar.gz you can manually click and download.

Best Regrads
Wei Zheng
by jlspzw
Mon Feb 19, 2024 8:37 pm
Forum: Main Forum
Topic: I-TASSER standalone suite installation
Replies: 7
Views: 105

Re: I-TASSER standalone suite installation

Dear Righteous,

How about this one https://zhanggroup.org/library/nr.tar.gz

Best Regards
Wei Zheng
by jlspzw
Mon Feb 19, 2024 6:23 pm
Forum: Main Forum
Topic: I-TASSER standalone suite installation
Replies: 7
Views: 105

Re: I-TASSER standalone suite installation

Hi Righteous,

Please change the line 102 in the download_lib.pl, the link from ftp://zhanglab.ccmb.med.umich.edu/download/nr.tar.gz to ftp://zhanglab.ccmb.med.umich.edu/library/nr.tar.gz , see if the new one works.

Best Regards
Wei Zheng