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BayeStab

This repo contains the code for our paper " BayeStab : Predicting effects of mutations on protein sta-bility with uncertainty quantification"

by Shuyu Wang*, Hongzhou Tang

Here we pioneered a deep graph neural network based method for predicting protein stability change upon mutation.

image

Dependency

  • Python 3.7
  • Pytorch
  • RDKit
  • Rosetta
  • numpy
  • CUDA
  • sklearn

Installation

BayeStab ΔΔG prediction is accomplished through a multi-step protocol. Each step relies on a specific third-party software that needs to be installed first. In the following, we outline the steps to install them.

Clone BayeStab

Clone BayeStab to a local directory.

git clone https://github.com/HongzhouTang/BayeStab.git

Install Rosetta 3

  1. Go to https://els2.comotion.uw.edu/product/rosetta to get an academic license for Rosetta.
  2. Download Rosetta 3.13 (source + binaries for Linux) from this site: https://www.rosettacommons.org/software/license-and-download
  3. Extract the tarball to a local directory from which Rosetta binaries can be called by specifying their full path.