Search found 43 matches
- Fri Jul 09, 2021 7:27 am
- Forum: Main Forum
- Topic: Generate Protein
- Replies: 8
- Views: 10863
Re: Generate Protein
Generally, a TM-score >=0.5 indicates that a protein has the correct global fold. Thus, in your case, the model seems to be low confidence. However, this is an estimation based on our statistics and may not reflect the actual TM-score.
- Sat May 29, 2021 3:37 pm
- Forum: Main Forum
- Topic: Usually how long will the I-TASSER standalone package take to predict protein structure?
- Replies: 1
- Views: 2673
Re: Usually how long will the I-TASSER standalone package take to predict protein structure?
Yes, this is a normal amount of time for modeling a protein by I-TASSER. If you are already running the simulations in parallel, you may try to run the -light simulations or specify the -hour cutoff, which may reduce the modeling accuracy though.
- Sat May 29, 2021 3:18 pm
- Forum: Main Forum
- Topic: I encountered some problems in the process of ResPRE building the contact matrix.
- Replies: 1
- Views: 2849
Re: I encountered some problems in the process of ResPRE building the contact matrix.
ResPRE predicts contact maps starting from the amino acid sequence, so it shouldn't be affected by missing regions in the PDB structure. If you input the full amino acid sequence, then the contact matrix will be 348x348. However, if you know the native structure of your protein, you probably don't n...
- Thu May 27, 2021 6:30 pm
- Forum: Main Forum
- Topic: output interpretation
- Replies: 7
- Views: 7546
Re: output interpretation
Depending on your target, the results may be slightly better for the web server as it includes a few more threading methods that aren't included in the downloadable version. This will influence the results for more distantly homologous threading targets, where it is difficult to identify suitable te...
- Thu May 27, 2021 2:00 pm
- Forum: Main Forum
- Topic: output interpretation
- Replies: 7
- Views: 7546
Re: output interpretation
1) No, as the standalone package uses Modrefiner to refine the protein conformation, while the online server uses a combination of several programs to perform the refinement. However, you may uncomment line 15 in the EMrefinement.pl included in the I-TASSER package, which will add hydrogens via HAAD...
- Wed May 26, 2021 1:20 pm
- Forum: Main Forum
- Topic: IonCom troubleshooting
- Replies: 2
- Views: 2684
Re: IonCom troubleshooting
Hello, Currently, we are catching up on some of the back logged jobs from when the server was down, so we have been experiencing delays for our online server. It seems the error should be with the PDB file you input to the program as PDB2Seq failed to extract the amino acid sequence from the PDB. Wo...
- Tue May 25, 2021 11:48 am
- Forum: Main Forum
- Topic: I have some questions about ResPRE
- Replies: 5
- Views: 7211
Re: I have some questions about ResPRE
Hello, Thank you for your interest in ResPRE! 1) The len() function will internally call __len__ to return the length of the object. Our implementation is: def __len__(self): return self.length The __getitem__ function will vary depending on your data loader implementation. We have not released our ...
- Mon May 24, 2021 5:10 pm
- Forum: Main Forum
- Topic: Processing consultation
- Replies: 3
- Views: 3041
Re: Processing consultation
GPCR-I-TASSER is back up and running and catching up on the back logged jobs at the moment!
- Thu May 20, 2021 1:32 pm
- Forum: Main Forum
- Topic: a problem in OUARK run
- Replies: 2
- Views: 2841
Re: a problem in OUARK run
Yes, we are currently working on fixing the problem and it should be back up today or tomorrow.
Thanks!
Thanks!
- Tue May 18, 2021 2:05 pm
- Forum: Main Forum
- Topic: Protein Models
- Replies: 2
- Views: 2631
Re: Protein Models
In your case, it seems that the generated model had a low confidence score. The estimated TM-score is 0.33, where TM-score ranges from 0-1 and a TM-score >=0.5 is generally used to indicate that the model has the correct global fold. Of course, it is not always true that a low c-score means a poor q...