Hi!
I need to predict binding site for around 400 proteins (GPCRs), and I wanted to use COACH for that. Since I assume it is not feasible to run this much calculations on the web server I installed the I-TASSER suite, downloaded the database via the perl script and managed to get a sensible result by testing on one of the proteins.
However, when I run my calculations in bulk (using snakemake), the progress becomes very slow - I only managed to calculate a fraction of the results in 4 days. The program is running on a server with 128 cores and 1 Tb of RAM, and I'm running all the jobs in parallel, so 128 proteins at once. Is there anything that I could do to speed up the process? Also, should I try to reduce the number of jobs for the sake of finishing each individual job faster?
Thank you,
Ilya