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:
- Raschka, Sebastian, Joseph Bemister‐Buffington, and Leslie A. Kuhn. "Detecting the native ligand orientation by interfacial rigidity: SiteInterlock." Proteins: Structure, Function, and Bioinformatics 84.12 (2016): 1888-1901.
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.
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
-
After clicking on the
Source code (zip)orSource code (tar.gz)download links, please navigate to your download folder and unpack the source code archive using your preferred archive-tool. -
Next, go into the unzipped
siteinterlock-masterdirectory, and install thesiteinterlockpackage by executingpython setup.py install(the top level directory in thesiteinterlock-masterfolder). -
You may verify your installation by opening a new terminal and executing the following command:
python -c 'import siteinterlock; print(siteinterlock.__version__)', which should print1.0.0. If you receive an -
Now, you will be able to use the SiteInterlock scripts provided in the
scripts/subdirectory from any location on your local drive.
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: [email protected]