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Bioinformatics Installation Instructions and Links

This document provides instructions for installing various bioinformatics software packages on Windows and links for downloading them. It outlines how to install MGLTools with AutoDockTools, AutoDock Vina by downloading the .msi file and running the installer, and Pyrx by downloading the executable file. It also provides instructions for installing Chimera by downloading the dmg file, and Open Babel by downloading the appropriate binary installer. Links are included for downloading each program.

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Vikas Sharma
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177 views2 pages

Bioinformatics Installation Instructions and Links

This document provides instructions for installing various bioinformatics software packages on Windows and links for downloading them. It outlines how to install MGLTools with AutoDockTools, AutoDock Vina by downloading the .msi file and running the installer, and Pyrx by downloading the executable file. It also provides instructions for installing Chimera by downloading the dmg file, and Open Babel by downloading the appropriate binary installer. Links are included for downloading each program.

Uploaded by

Vikas Sharma
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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Bioinformatics Installation Instructions and Links

MGLTools in Windows:
 Visit the MGLTools download page and download the mgltools_win32_*_Setup.exe.
 Double-click on the downloaded file to start the installation process1.
 AutoDockTools is available as the part of MGLTools
AutoDock Vina:
 Download the .msi of AutoDock Vina.
 Double-click on the downloaded .msi file.
 Select an appropriate location to install and wait to finish.
 This will create a new folder named Vina-xxx. There you will find vina.exe which will
be required at the time of its execution.
 Now, you can see shortcuts would have been created on your desktop. Double click
Autodock-Tools shortcut to start the graphical user interface. There you can prepare your
receptor and ligands for docking2. After you prepare all the files, keep them in the same
folder. Open a command prompt, provide the full path to the vina executable (vina.exe),
and run the command.
 The Python Molecular Viewer (PMV), a general-purpose molecular viewer
 Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for
visualization and analysis of molecular structures. MGLTools comprises:
o The Python Molecular Viewer (PMV), a general purpose molecular viewer
o AutoDockTools (ADT) a set of PMV commands specifically developed to support
AutoDock users
o Vision, a visual programing environment.
Pyrx installation for windows
Pyrx is another virtual screening software that also offers to perform docking using Autodock
Vina. In this article, we will install Pyrx on Windows.
Downloading Pyrx
Download the binary file from here. An executable file namely, ‘PyRx-0.8-Setup.exe’ will be
downloaded.
Installing Pyrx
 Double-click on the executable or right-click à ‘Run as
administrator’.
 It will ask for the location to install the software. Choose
appropriately.
 Click ‘Next’. Let the installation finish. It will take a few minutes.
 Click ‘Finish’.
No Mac installation for Pyrx
Chimera Installation
 Click the share link to download the latest version of Chimera.
 chimera-1.11.2-mac_x11.dmg for both mac and windows users.
 Download the 64-bits from current production release, *.exe for windows, *.dmg for Mac
OS and *.bin for linux.
 There is no 32 bits release for Chimeara only one release is available for small
systems.
Open Babel installation
Binary Package (Recommended):

 Download the latest version of Open Babel from GitHub.


 Choose the appropriate binary installer for your system (64-bit is preferred, but 32-bit is also
available).
 Install the downloaded package, which includes command-line tools and a graphical user
interface (GUI).

LINKS
*AutoDock MGL Tools [Downloads – AutoDock Vina (scripps.edu)]
*AutoDock Vina [Downloads – AutoDock Vina (scripps.edu)]
*Pyrx [PyRx - Virtual Screening Tool download | SourceForge.net]
*Pymol visualization tool [PyMOL | pymol.org]
*Chimera [Download UCSF Chimera]
*Openbabel [Releases · openbabel/openbabel (github.com)]

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