PaRSnIP

PaRSnIP is a sequence-based protein solubility predictor.

Motivation

Protein solubility can be a decisive factor in both research and production efficiency, and in silico sequence-based predictors, which can accurately estimate solubility outcomes, are highly sought of.

Installation

Requirements

• R (https://www.r-project.org)
  • R libraries
    • bio3d
    • stringr
    • Interpol
    • zoo
    • h2o (version 3.10.0.8) (https://cran.r-project.org/web/packages/h2o/index.html) (see "Old sources")
• SCRATCH (version SCRATCH-1D release 1.1) (http://scratch.proteomics.ics.uci.edu, Downloads: http://download.igb.uci.edu/#sspro)

Run

PaRSnIP can be run in the command line

Three input arguments are necessary to run the software.

1. Protein sequence of interest in fasta format (https://en.wikipedia.org/wiki/FASTA_format)
2. SCRATCH run path (usually it is in the directory where you installed SCRATCH adding the following SCRATCH-1D_1.1/bin/run_SCRATCH-1D_predictors.sh)
3. The PaRSnIP h2o model (PaRSnIP_training_model)

Execute in the command line

R --vanilla < PaRSnIP.R argument1 argument2 argument3

(Example: R --vanilla < /home/user/software/PaRSnIP.R test_protein.fa /home/user/software/SCRATCH/SCRATCH-1D_1.1/bin/run_SCRATCH-1D_predictors.sh /home/user/software/PaRSnIP_training_model)

Result

Probability that the protein test sequence is soluble will be saved in file result.txt

Tests

R --vanilla < PaRSnIP.R P21.fasta ..../SCRATCH-1D_1.1/bin/run_SCRATCH-1D_predictors.sh PaRSnIP_training_model output.txt

Reference

Reda Rawi, Raghvendra Mall, Khalid Kunji, Chen-Hsiang Shen, Peter D Kwong, Gwo-Yu Chuang; PaRSnIP: sequence-based protein solubility prediction using gradient boosting machine, Bioinformatics, Volume 34, Issue 7, 1 April 2018, Pages 1092–1098, https://doi.org/10.1093/bioinformatics/btx662

Contact

Reda Rawi: reda.rawi@nih.gov