minghuilab / PremPLI

PremPLI

About

PremPLI predicts the effects of single mutations on protein-ligand interactions by calculating the binding affinity changes quantitatively. It can be used for guiding the design of ligand-binding proteins, identifying and understanding disease driver mutations, and finding potential resistance mutations for different drugs. The 3D structure of a protein-ligand complex is required for performing the prediction.

Scoring mutations with PremPLI

We recommend that most users who just want to obtain PremPLI predictions use PremPLI website to obtain scores.

Source code releases

You can download releases on github.

Installation

I. PREREQUISITES

PremPLI requires the following software and packages.

1. PROVEAN

   This is available at the PROVEAN website.

   http://provean.jcvi.org/index.php/

2. NCBI BLAST 2.4.0

   This is available at the NCBI ftp site.

   ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.4.0/

3. DSSP

   This is available at the DSSP website.

   https://swift.cmbi.umcn.nl/gv/dssp/

4. FoldX

   This is available at the FoldX website.

   http://foldxsuite.crg.eu/

5. VMD

   This is available at the VMD website.

   https://www.ks.uiuc.edu/Research/vmd/

6. UCSF Chimera

   This is available at the Chimera website.

   http://www.cgl.ucsf.edu/chimera/

7. Arpeggio

   This is available at the Arpeggio website.

   https://bitbucket.org/harryjubb/arpeggio/

8. XLOGP3

   This is available at the XLOGP3 website.

   http://sioc-ccbg.ac.cn/skins/ccbgwebsite/software/xlogp3/

9. Python packages: pandas, biopython, sklearn and rpy2

   To install these packages you can use the following command:

$ conda install -c conda-forge pandas
$ conda install -c conda-forge biopython
$ conda install -c conda-forge scikit-learn
$ conda install -c r rpy2

10. R packages: randomForest and stringr

$ install.packages('randomForest')
$ install.packages('stringr')

II. INSTALLATION INSTRUCTIONS

1. Download and/or install prerequisites described above.

2. Download and unpack the distribution:

$ wget https://github.com/minghuilab/PremPLI/archive/v1.0.tar.gz
$ tar -zxvf v1.0.tar.gz

3. Change to the source directory:

$ cd PremPLI-1.0/v1.0

4. Change the path parameters in PremPLI.py:

workdir = Your working directory
pathvmd = path for running VMD software  # /usr/local/bin/vmd
pathmkdssp = path for running DSSP software  # /usr/local/bin/mkdssp
pathpsiblast = path for running PSI-BLAST software  # /usr/local/bin/blast/psiblast
pathblastdb = path for blastdb  # /usr/local/bin/blastdb/nr
pathprovean = path for PROVEAN software  # /usr/bin/provean.sh
patharpeggio = path for Arpeggio software  # /usr/local/bin/arpeggio/arpeggio.py
pathxlogp3 = path for running XLOGP3 software  # /usr/local/bin/

    The FoldX software needs to be installed in the working directory.

III. RUNNING PremPLI

$ python PremPLI.py -i 2021031002563493343426069

Platform

PremPLI is only intended to run on linux operating systems.

Issues

You will need to have Python 2.7 and R 3.4.0 (or higher) installed.