Zhanglab forum

also, when you do like what said, then run commands like the following ~/Desktop/fatin/I-TASSER5.1/I-TASSERmod$ ./runI-TASSER.pl -libdir /home/user/Desktop/fatin/I-TASSER5.1/ITLIB -seqname Test -datadir /home/user/Desktop/fatin/I-TASSER5.1/Test -outdir /home/user/Desktop/fatin/I-TASSER5.1/Test if yo...

Can you make a folder that named as "Test" or others instead of "LAN_01_018,1.10.20.10-FF-000011,564-639" and put you sequence in that folder, rename the sequence file as seq.fasta, do not just put LAN_01_018,1.10.20.10-FF-000011,564-639 into the folder, I am not sure the problem...

Hi Francisco I think I got the problem, in some old Fortran program, the library path are set at most 100 characters, thus you full AAA.sec path should be /ibex/scratch/projects/c2102/mutation_classifier/programs/cITASSER/C-I-TASSER-1.0/ITLIB2/summary/AAA.sec, which over the limitation. The simple s...

We currently have lots of jobs pending, thus the responding time may longer than usual, I believe u already start to use C-QUARK now

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/