Zhanglab forum

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

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

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...

can you attach you sequence here? we can not find problem from the pasted sequence, Than you.

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...

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/

Dear user,
you can download the C-QUARK package at https://zhanglab.dcmb.med.umich.edu/C-Q ... nload.html
Best
ITteam

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...

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...

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 ...