RaptorX is a protein structure prediction server developed by Xu group, excelling at predicting 3D structures for protein sequences without close homologs in the Protein Data Bank (PDB). Given an input sequence, RaptorX predicts its secondary and tertiary structures as well as solvent accessibility and disordered regions.

References:

• Wang Z, Zhao F, Peng J, Xu J. Protein 8-class secondary structure prediction using conditional neural fields. Proteomics. 2011 Oct;11(19):3786-92.

• RaptorX Main Site

• Module Name: raptorx (see the modules page for more information)
• Multithreaded
• Example files in $RAPTORX_EXAMPLES

RaptorX uses psiblast, which can utilize multiple cpus to accelerate alignments.

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

[user@biowulf]$ sinteractive --cpus-per-task=8
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

[user@cn3144 ~]$ module load raptorx

[user@cn3144 ~]$ cp $RAPTORX_EXAMPLES/lysozyme .
[user@cn3144 ~]$ run_raptorx-ss3.pl lysozyme

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

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

#!/bin/bash
module load raptorx
run_raptorx-ss8.pl blah.fasta

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=8 raptorx.sh

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

run_raptorx-ss8.pl protein1.fasta
run_raptorx-ss8.pl protein2.fasta
run_raptorx-ss8.pl protein3.fasta
run_raptorx-ss8.pl protein4.fasta

Submit this job using the swarm command.

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