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A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed by graph theoretic constraint counting on the covalent and noncovalent bond network. Raschka et al. (2016) Proteins: Structure, Function, and Bioinformatics
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README.md

SiteInterlock

SiteInterlock Logo

A novel approach to pose selection in protein-ligand docking based on graph theory.

siteinterlock is a Python package for selecting near-native protein-ligand docking poses based upon the hypothesis that interfacial rigidification of the protein-ligand interface is an important characteristic that can detect the native ligand binding mode.

The siteinterlock package was developed by Sebastian Raschka in the Protein Structural Analysis & Design Laboratory at Michigan State University. For additional information on the theory behind the SiteInterlock project, please refer to the accompanying research publication:

Installation

The siteinterlock package is compatible with Python 2.7.x and Python 3.2 or newer; we recommend using Python 3.5. The package itself does not require external dependencies or libraries. If you don't already have Python installed on your system, you can find more information on how to obtain and install Python at https://www.python.org/downloads/.

To produce the input files that are required for the SiteInterlock analysis, you will need to have MSU ProFlex installed. MSU ProFlex (formerly called FIRST) predicts the rigid and flexible regions in a protein structure, given a Protein Data Bank (PDB) file, which you can process according to ProFlex instructions to add the necessary polar hydrogen atom coordinates. You can find more information about obtaining and installing ProFlex at http://kuhnlab.bmb.msu.edu/software/proflex/index.html.

Installing siteinterlock from source

Please make sure that you are using Python 2.7.x or Python 3.2 or newer when you are installing and using siteinterlock. You can check the version tag of your Python installation by executing python --version or python3 --version from the command line terminal.

You can obtain the latest, stable release of siteinterlock from GitHub at https://github.com/psa-lab/siteinterlock/releases

  1. After clicking on the Source code (zip) or Source code (tar.gz) download links, please navigate to your download folder and unpack the source code archive using your preferred archive-tool.

  2. Next, go into the unzipped siteinterlock-master directory, and install the siteinterlock package by executing python setup.py install (the top level directory in the siteinterlock-master folder).

  3. You may verify your installation by opening a new terminal and executing the following command: python -c 'import siteinterlock; print(siteinterlock.__version__)', which should print 1.0.0. If you receive an

  4. Now, you will be able to use the SiteInterlock scripts provided in the scripts/ subdirectory from any location on your local drive.

Documentation

You can find a detailed user guide in the package documentation that is hosted at http://psa-lab.github.io/siteinterlock/index.html.

Alternatively, you can view the documentation offline after downloading siteinterlock and opening the index.html file that is located in the docs/html/ subdirectory in your preferred web browser.



Copyright (C) 2016 Michigan State University
Developed in the Protein Structural Analysis & Design Laboratory
Contact Email: kuhnlab@msu.edu

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