Search found 32 matches

by robpearc
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: 153

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.
by robpearc
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: 83

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...
by robpearc
Thu May 27, 2021 6:30 pm
Forum: Main Forum
Topic: output interpretation
Replies: 7
Views: 421

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...
by robpearc
Thu May 27, 2021 2:00 pm
Forum: Main Forum
Topic: output interpretation
Replies: 7
Views: 421

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...
by robpearc
Wed May 26, 2021 1:20 pm
Forum: Main Forum
Topic: IonCom troubleshooting
Replies: 2
Views: 258

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...
by robpearc
Tue May 25, 2021 11:48 am
Forum: Main Forum
Topic: I have some questions about ResPRE
Replies: 5
Views: 241

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 ...
by robpearc
Mon May 24, 2021 5:10 pm
Forum: Main Forum
Topic: Processing consultation
Replies: 3
Views: 329

Re: Processing consultation

GPCR-I-TASSER is back up and running and catching up on the back logged jobs at the moment!
by robpearc
Thu May 20, 2021 1:32 pm
Forum: Main Forum
Topic: a problem in OUARK run
Replies: 2
Views: 210

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!
by robpearc
Tue May 18, 2021 2:05 pm
Forum: Main Forum
Topic: Protein Models
Replies: 2
Views: 267

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...
by robpearc
Mon May 17, 2021 3:56 am
Forum: Main Forum
Topic: I-TASSER suit stuck at the step of "running pairing"
Replies: 3
Views: 245

Re: I-TASSER suit stuck at the step of "running pairing"

I-TASSER will run on your CPU resources. Even so, this is an excessively long running time. If there was no error in the program, it might be best to check your server to make sure everything is running properly.