DeepSol


Protein solubility plays a vital role in pharmaceutical research and production yield. For a given protein, the extent of its solubility can represent the quality of its function, and is ultimately defined by its sequence. Thus, it is imperative to develop novel, highly accurate in silico sequence-based protein solubility predictors.

DeepSol is a novel Deep Learning based protein solubility predictor. The backbone of our framework is a Convolutional Neural Network (CNN) that exploits k-mer structure and additional sequence and structural features extracted from the protein sequence.

Availability: DeepSol is also available as


DeepSol: A Deep Learning Framework for Sequence-Based Protein Solubility Prediction

Motivation

Protein solubility can be a decisive factor in both research and production efficiency. Novel in silico, accurate, sequence-based protein solubility predictors are highly sought.

Installation

Requirements

This step will install all the dependencies required for running DeepSol in an Anaconda virtual environment locally. You do not need sudo permissions for this step.

  • Install Anaconda

    1. Download Anaconda (64 bit) installer python3.x for linux :https://www.anaconda.com/download/#linux
    2. Run the installer : bash Anaconda3-5.0.1-Linux-x86_64.sh and follow the instructions to install anaconda at your preferred location
    3. Need conda > 4.3.30 (If conda already present but lower than this version do: conda upgrade conda)
  • Creating the environment

    1. Run git clone https://github.com/sameerkhurana10/DSOL_rv0.2.git
    2. Run cd DSOL_rv0.2
    3. Run export PATH=/bin:$PATH
    4. Run conda env create -f environment.yml
    5. Run source activate dsol


DSOL Discussion