Search found 38 matches

by robpearc
Thu Jul 22, 2021 7:27 pm
Forum: Main Forum
Topic: job S629837
Replies: 1
Views: 69

Re: job S629837

We apologize for the delay! Your results are available at https://zhanggroup.org/I-TASSER/output/S629837/.
by robpearc
Thu Jul 22, 2021 7:24 pm
Forum: Main Forum
Topic: Job not yet received
Replies: 1
Views: 81

Re: Job not yet received

We are currently catching up on previous jobs, which have been delayed due to a high number of jobs for a related project. Your job should be completed in the order that it was received.

Thanks!
by robpearc
Wed Jul 21, 2021 4:41 am
Forum: Main Forum
Topic: Getting information about model ranked 2 i-Tasser
Replies: 2
Views: 60

Re: Getting information about model ranked 2 i-Tasser

The different models are generated by clustering all of the conformations produced during the folding simulations, so the templates identified for model 1 should be identical to those identified for models 2, 3, 4 etc. The other information, such as the biological function prediction may be obtained...
by robpearc
Fri Jul 16, 2021 8:01 am
Forum: Main Forum
Topic: How to explain the predicted 3D structures
Replies: 3
Views: 74

Re: How to explain the predicted 3D structures

I'm not quite sure I understand your question. Would you be able to provide some more information on what you mean? It looks like the two sequences are different and produce different modeling results, although they share several regions with high similarity as the sequences are similar.

Thanks!
by robpearc
Fri Jul 16, 2021 7:55 am
Forum: Main Forum
Topic: Error during SPRINGDB instalaltion
Replies: 1
Views: 36

Re: Error during SPRINGDB instalaltion

This may be an issue with f2py. Have you tried compiling the program using gfortran -static -O3 -ffast-math -lm -o NWalign NWalign.f or g77 -static -O3 -lm -o NWalign NWalign.f, which is recommended for compilation?
by robpearc
Fri Jul 09, 2021 7:27 am
Forum: Main Forum
Topic: Generate Protein
Replies: 3
Views: 65

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.
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: 210

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: 119

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: 509

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: 509

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...