Search found 247 matches
- Thu Jul 08, 2021 3:47 pm
- Forum: Main Forum
- Topic: C-Quark local installation processing time for 30 amino acid peptide?
- Replies: 1
- Views: 2052
Re: C-Quark local installation processing time for 30 amino acid peptide?
It may takes less than one day for a protein with only 30 amino acid I believe. The library is slightly big, but it worth using C_QUARK than QUARK, C-UQARK performance is much better than QUARK
- Wed Jul 07, 2021 1:37 pm
- Forum: Main Forum
- Topic: how to download QUARK locally?
- Replies: 4
- Views: 2636
Re: how to download QUARK locally?
BTW, C-QUARK does not support multi-cpu, that means if you have two cpus, then you can run tow proteins at the same time, then each job will occupy one cpu. if you have multi-core or a cluster, 1K sequence can run parallel
- Wed Jul 07, 2021 1:33 pm
- Forum: Main Forum
- Topic: how to download QUARK locally?
- Replies: 4
- Views: 2636
Re: how to download QUARK locally?
Hi Xiao, The C-QUARK indeed need over 4 hours to get a protein, some even more longer time. QE is full ab initio pipeline without any templates. it runs DeepMSA and PSIBLAST for sequence homologous collection, where later will be used for contact prediction by deep-learning, those steps are not rela...
- Wed Jul 07, 2021 1:26 pm
- Forum: Main Forum
- Topic: error when running i-tasser
- Replies: 5
- Views: 4693
Re: error when running i-tasser
can you attach you sequence here? we can not find problem from the pasted sequence, Than you.
- Tue Jul 06, 2021 7:45 pm
- Forum: Main Forum
- Topic: Beta Structure Prediction
- Replies: 1
- Views: 1871
Re: Beta Structure Prediction
The helix and strand shown in right is predicted results, there is no guarantee that they are 100% correct. Furthermore, the predicted helix and strand are very short, I am not sure those are reasonable results. I-TASSER used a more comprehensive force field fold protein, thus the model secondary st...
- Tue Jul 06, 2021 5:57 pm
- Forum: Main Forum
- Topic: Regarding GPCR-HGmod
- Replies: 1
- Views: 1784
Re: Regarding GPCR-HGmod
GPCR-HGmod is a very old database, to build the most stat-of-the-art model, You can submit the sequence to https://zhanglab.dcmb.med.umich.edu/C-I-TASSER/
- Tue Jul 06, 2021 5:44 pm
- Forum: Main Forum
- Topic: how to download QUARK locally?
- Replies: 4
- Views: 2636
Re: how to download QUARK locally?
Dear user,
you can download the C-QUARK package at https://zhanglab.dcmb.med.umich.edu/C-Q ... nload.html
Best
ITteam
you can download the C-QUARK package at https://zhanglab.dcmb.med.umich.edu/C-Q ... nload.html
Best
ITteam
- Mon Jul 05, 2021 2:10 pm
- Forum: Main Forum
- Topic: Problems with C-QUARK standalone
- Replies: 11
- Views: 12922
Re: Problems with C-QUARK standalone
If the python has issue, then you can try /bin/python2 /mnt/disk/C-QUARK-1.0/contact/DeepMSA/scripts/build_MSA.py /mnt/disk/C-QUARK-1.0/example/seq.fasta -hhblitsdb=/mnt/disk/ITLIB/uniclust30/uniclust30_2017_04 -jackhmmerdb=/mnt/disk/ITLIB/uniref90/uniref90.fasta -hmmsearchdb=/mnt/disk/ITLIB/metaclu...
- Mon Jul 05, 2021 2:08 pm
- Forum: Main Forum
- Topic: Problems with C-QUARK standalone
- Replies: 11
- Views: 12922
Re: Problems with C-QUARK standalone
Dear user, During the program running, there are many files created by the program will locate in /tmp/skyto and /tmp/. Do NOT and make sure your system will NOT clean those two folders! It is not difficult to run DeepMSA you can do export HHLIB=/mnt/disk/C-QUARK-1.0/contact/DeepMSA then run /mnt/di...
- Mon Jul 05, 2021 1:53 pm
- Forum: Main Forum
- Topic: Errors in threading programs in standalone C-I-TASSER-1.0
- Replies: 3
- Views: 3725
Re: Errors in threading programs in standalone C-I-TASSER-1.0
Dear user, It may be caused by some uncomplete library file could you do "ls /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/ITLIB2" and "ls /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/ITLIB2/summary" see if ...