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
Search found 247 matches
- Wed Jan 25, 2023 2:45 pm
- Forum: Main Forum
- Topic: unexpected EOF in DeepMSA
- Replies: 1
- Views: 18309
- Sat Jan 14, 2023 1:55 am
- Forum: Main Forum
- Topic: Protein-Peptide binding predictions with DeepMSAFold-Multimer
- Replies: 1
- Views: 13569
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
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
- Sat Jan 14, 2023 1:48 am
- Forum: Main Forum
- Topic: How can I input multi-chain sequence as fasta?
- Replies: 5
- Views: 16507
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
We are working on it, and the package will be available after our manuscript has been published.
Best
IT Team
- Thu Jan 12, 2023 1:17 pm
- Forum: Main Forum
- Topic: Bug in I-TASSER-MD download_lib.pl
- Replies: 1
- Views: 12994
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
Thank you for reporting the bug. We will fix the issue.
Best
IT Team
- 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: 13199
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...
- Thu Jan 05, 2023 4:51 am
- Forum: Main Forum
- Topic: apply post translational modification in 3D structure
- Replies: 1
- Views: 12493
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
Based on our knowledge, there is no 3D modeling method that can model the structure of PTM sites.
Best
IT team
- Tue Dec 27, 2022 6:15 pm
- Forum: Main Forum
- Topic: How can I input multi-chain sequence as fasta?
- Replies: 5
- Views: 16507
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
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
- Sat Dec 24, 2022 6:18 am
- Forum: Main Forum
- Topic: No result obtained
- Replies: 1
- Views: 9946
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
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
- Tue Dec 13, 2022 8:25 pm
- Forum: Main Forum
- Topic: I-TASSER-MR not working
- Replies: 1
- Views: 7667
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
The original author has left our lab, and our IT team is working to check the server. Thank you.
Best
IT team
- Fri Dec 09, 2022 9:23 pm
- Forum: Main Forum
- Topic: Take into account pLDDT into TM-score
- Replies: 1
- Views: 7115
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...