rosettafold2na

Protein–RNA and protein–DNA complexes play critical roles in biology. Despite considerable recent advances in protein structure prediction, the prediction of the structures of protein–nucleic acid complexes without homology to known complexes is a largely unsolved problem. Here we extend the RoseTTAFold machine learning protein-structure-prediction approach to additionally predict nucleic acid and protein–nucleic acid complexes. We develop a single trained network, RoseTTAFoldNA, that rapidly produces three-dimensional structure models with confidence estimates for protein–DNA and protein–RNA complexes. (Summary from the program web page.)

The official web page: https://github.com/uw-ipd/RoseTTAFold2NA

Notes:

The package is available on the WOLF, SOKAR, and MetaCentrum clusters.

• ngpus > 0

Available tools:

• run_RF2NA.sh

Typical workflow:

1. Create a new job directory
2. Enter the job directory
3. Copy an input FASTA file in the job directory
4. Create a job script in in the job directory (see below)
5. Submit a job into a batch system (see below), you need to specify required resources !!!
6. Wait until the job completes (see outputs of commands pjobs, pinfo)
7. Resulting models are in specified subdirectory. The log from the RoseTTAFold2NA program is in the *.stdout file.

Example script (my_job)

#!/usr/bin/env infinity-env

# activate the module
module add rosettafold2na

# run the prediction with default setup (see run_RF2NA.sh -h for the list of options)
run_RF2NA.sh rna_pred rna_binding_protein.fa R:RNA.fa

Job submission on the WOLF cluster (one day max)

$ psubmit alphafold my_job ncpus=8 ngpus=1 mem=50gb

Job submission on the SOKAR cluster (up to 30 days)

$ psubmit alphafold my_job ncpus=8 ngpus=1 mem=50gb walltime=2d

Job submission on the MetaCentrum (one day max)

$ psubmit gpu my_job ncpus=8 ngpus=1 mem=50gb

• alphafold is the name of batch queue, this queue is generally dedicated for structure prediction jobs
• ncpus - number of requested CPUs, rosettafold2 is not well optimized for large number of CPUs, thus, keep this number low (about 8)
• ngpus - number of requested GPUs, rosettafold2 must run at least on one GPU
• mem - amount of system memory
• walltime - maximum job duration in days (d) or hours (h)