Search found 107 matches

by jlspzw
Wed Jan 25, 2023 2:45 pm
Forum: Main Forum
Topic: unexpected EOF in DeepMSA
Replies: 1
Views: 115

Re: unexpected EOF in DeepMSA

Dear user,

We have contacted the author of DeepFold, and all the related issues, you can report to him if you don't get feedback from him here.
His email address is robpearc@umich.edu .

Thank you.

Best
IT Team
by jlspzw
Sat Jan 14, 2023 1:55 am
Forum: Main Forum
Topic: Protein-Peptide binding predictions with DeepMSAFold-Multimer
Replies: 1
Views: 248

Re: Protein-Peptide binding predictions with DeepMSAFold-Multimer

Dear user,

We have temporarily changed it to 10, so you can try it if it works. For very short peptides (<10AA), we are not sure if it could get a reasonable result since we do not have any benchmark on it.

Best
IT Team
by jlspzw
Sat Jan 14, 2023 1:48 am
Forum: Main Forum
Topic: How can I input multi-chain sequence as fasta?
Replies: 3
Views: 448

Re: How can I input multi-chain sequence as fasta?

Dear user,

We are working on it, and the package will be available after our manuscript has been published.

Best
IT Team
by jlspzw
Thu Jan 12, 2023 1:17 pm
Forum: Main Forum
Topic: Bug in I-TASSER-MD download_lib.pl
Replies: 1
Views: 236

Re: Bug in I-TASSER-MD download_lib.pl

Dear user,

Thank you for reporting the bug. We will fix the issue.

Best
IT Team
by jlspzw
Wed Jan 11, 2023 1:06 am
Forum: Main Forum
Topic: Replicas picked for clustering and model genaration while using I-TASSER
Replies: 2
Views: 261

Re: Replicas picked for clustering and model genaration while using I-TASSER

Dear user, Thank you for using the I-TASSER. You can find some explanations on our CASP14 abstract, https://predictioncenter.org/casp14/doc/CASP14_Abstracts.pdf. Please see the Zhang-Server section. The numbers 8 and 3 are decided based on a benchmark test that aims to optimize the final model quali...
by jlspzw
Thu Jan 05, 2023 4:51 am
Forum: Main Forum
Topic: apply post translational modification in 3D structure
Replies: 1
Views: 328

Re: apply post translational modification in 3D structure

Dear user,

Based on our knowledge, there is no 3D modeling method that can model the structure of PTM sites.

Best
IT team
by jlspzw
Tue Dec 27, 2022 6:15 pm
Forum: Main Forum
Topic: How can I input multi-chain sequence as fasta?
Replies: 3
Views: 448

Re: How can I input multi-chain sequence as fasta?

Dear user,

D-I-TASSER currently does not support multi-chain modeling. We are working on a new server and will let it be released soon.

You can try this link temporarily, but the waiting time may be slightly longer since we are not complete it yet.

https://zhanggroup.org/DeepMSAFold/

Best
IT Team
by jlspzw
Sat Dec 24, 2022 6:18 am
Forum: Main Forum
Topic: No result obtained
Replies: 1
Views: 430

Re: No result obtained

Dear user,

Our server recently had a large amount jobs. You may want to send an email to yangzhanglab@umich.edu for advance help with the job running. Please attach the jobid to the email.

Best
IT Team
by jlspzw
Tue Dec 13, 2022 8:25 pm
Forum: Main Forum
Topic: I-TASSER-MR not working
Replies: 1
Views: 572

Re: I-TASSER-MR not working

Dear user,

The original author has left our lab, and our IT team is working to check the server. Thank you.

Best
IT team
by jlspzw
Fri Dec 09, 2022 9:23 pm
Forum: Main Forum
Topic: Take into account pLDDT into TM-score
Replies: 1
Views: 530

Re: Take into account pLDDT into TM-score

Dear user, If you make sure some areas are disordered, you can remove those residues both from the model and native, only keep the core region that you mentioned, then you will get a good score. The pLDDT score and TM-score are completely different things, pLDDT score is a predicted LDDT score, so w...