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Last pushed: 2 years ago
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Virtual screening software and scripts for receptor- and ligand-based screening
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#Virtual Small Molecule Screening

This repository provides access to free pre-installed software and scripts for virtual small molecule screening. Several public tools for receptor- and ligand-based screening are included, e.g. AutoDock Vina, CyScore, OpenBabel, ToxTree, QeD and Filter-it, among others (see details on software and usage below). An example screening can be started by executing the "run_screening.sh" script (see section "Quick Start" below).


#Integrated Pre-installed Software

  • OpenBabel:
    A chemical toolbox for file format conversions, ligand-based
    screening, molecular superimposition, partial charge calculation etc.,
    provided under the GNU General Public License
    (see http://openbabel.org/ for details from the developpers)

    Quick start: Type "babel --help" at the command prompt

  • AutoDock Vina:
    A molecular docking software provided under the Apache license
    (see http://vina.scripps.edu for details from the developpers)

    Quick start: Type "vina --help" at the command prompt

  • CyScore:
    An empirical scoring function for accurate protein-ligand binding
    affinty prediction
    (see http://clab.labshare.cn/software/cyscore.html for details
    from the developpers)

    Quick start: Type "Cyscore" at the command prompt

  • ToxTree:
    An open source application to estimate the toxic hazard for small molecules
    (see http://toxtree.sourceforge.net for details from the developpers)

    Quick start:
    Type "java -jar /home/Toxtree-v2.6.13/Toxtree/Toxtree-2.6.13.jar --help"
    at the command prompt

  • QeD:
    A software for quantitative estimation of drug-likeness, provided
    by Silicos-it under the GNU Lesser General Public License
    (see http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/software.html
    for details from the developpers:

    Quick start: Launch "python" and type:

    ```from silicos_it.descriptors import qed
    from rdkit import Chem
    m = Chem.MolFromSmiles('c1ccccc1')
    qed.default(m)```
    
  • Filter-it:
    A program for filtering out molecules with unwanted chemical or
    structural properties, provided by Silicos-it under the
    GNU Lesser General Public License
    (see http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/software.html
    for details from the developpers)

    Quick start: Type "filter-it --help" at the command prompt


#Quick Start

After installing the Docker software on your system (see https://docs.docker.com), you can download the screening container and start an interactive session by typing "docker run -it vscreening/screening" at the command prompt. To run an example receptor-based screening by docking compounds from the NCI Diversity Set 2 compound library into the HIV-1 protease (hsg1.pdbqt file in the home/examples folder), a fully automated script
can be executed by entering:

./run_screening.sh

After the screening has been completed, the poses of the docked molecules can
be found in the home/docking_results folder and the log-files are stored in
the log_files folder (type "cd /home/docking_results" or "cd /home/log_files""). The list of top-ranked molecules and their associated docking scores can be obtained by running the
"screening_get_top.py" script in the home-folder (the number of top-ranked
molecules to be shown, e.g. 10, is required as parameter):

cd /home
python screening_get_top.py 10

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vscreening

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