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.

Protein sequence of interest in fasta format (https://en.wikipedia.org/wiki/FASTA_format)
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)
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

raghvendra5688/PaRSnIP