Open-Source Computational Structural Biology Framework

References:

• M. Biasini, T. Schmidt, S. Bienert, V. Mariani, G. Studer, J. Haas, N. Johner, A.D. Schenk, A. Philippsen and T. Schwede OpenStructure: an integrated software framework for computational structural biology. Acta Cryst., 2013.
• M. Bertoni, F. Kiefer, M. Biasini, L. Bordoli, T. Schwede, Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports, 2017.

• OpenStructure Main Site

• Module Name: OpenStructure
• Tunnel is needed for jupyter here, follow here
• This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.
• Environment variables set
  • OpenStructure_EXAMPLES
• Example files in $OpenStructure_EXAMPLES

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive -c 16 --mem=46G --gres=lscratch:50  --time=4:00:00 -T  
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
Created 1 generic SSH tunnel(s) from this compute node to
biowulf for your use at port numbers defined
in the $PORTn ($PORT1, ...) environment variables.


Please create a SSH tunnel from your workstation to these ports on biowulf.
On Linux/MacOS, open a terminal and run:

    ssh  -L 42791:localhost:42791 abc@biowulf.nih.gov

[user@cn3144 ~]$ module load OpenStructure

[user@cn3144 ~]$ jupyter 

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. OpenStructure.sh). For example:

#!/bin/bash
set -e
module load OpenStructure
ost compare-structures -m ./demos/data/sdh.pdb -r ./demos/data/sdh-complete.pdb -o test.out --lddt --local-lddt

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] OpenStructure.sh

Create a swarmfile (e.g. OpenStructure.swarm). For example:

ost compare-structures -m ./demos/data/sdh.pdb -r ./demos/data/sdh-complete.pdb -o test.out --lddt --local-lddt
ost compare-structures -m ./demos/data/sdh2.pdb -r ./demos/data/sdh-complete.pdb -o test.out --lddt --local-lddt

Submit this job using the swarm command.

swarm -f OpenStructure.swarm [-g #] [-t #] --module OpenStructure