Docking and simulation are two of the methods that are most widely used in bioinformatics. In this article, we provide all important links to the software for docking and simulation where you can easily download them.

Let’s start with some important docking software that is most widely used.

Docking software

• Autodock Vina
  http://vina.scripps.edu/download.html
  Here, you will find different packages for Windows, Linux, and macOS including the source code.
• Autodock 4
  http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
  Here, you will find different packages for Windows, Linux, Sun Solaris, and macOS including the source code.
• MGLTools
  http://mgltools.scripps.edu/downloads
  Here, you will find different packages for Windows, Linux, and macOS including the source code.
• Pyrx
  https://pyrx.sourceforge.io/
  It has different packages including both free and paid ones.
• Glide
  https://www.schrodinger.com/products/glide
  This is not freely accessible, you will have to purchase the license.
• GOLD Suite
  https://www.ch.cam.ac.uk/computing/software/gold-suite
  This software is also not freely available.

Docking output analysis software

• Pymol
  https://pymol.org/2/
  Here, you can find the latest version of Pymol for different platforms.
• Discovery Studio Visualizer
  https://discover.3ds.com/discovery-studio-visualizer-download

Simulation Software

• GROMACS
  https://manual.gromacs.org/documentation/ (For latest releases)
  https://www.gromacs.org/Downloads_of_outdated_releases (For outdated releases)
• NAMD
  https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD
  Here, you will find different versions. Select appropriately keeping in mind the architecture (62-bit/32-bit) of your system.
• VMD
  https://www.ks.uiuc.edu/Research/vmd/
  You may have to fill out a registration form to download.
• AMBER
  https://ambermd.org/GetAmber.php
  You can download and install it via conda or source code.
• CHARMM
  https://charmm.chemistry.harvard.edu/charmm_lite.php
  Here, you will have to fill out a charmm nonprofit/academic license.

MD Simulation plot visualization software

• xmgrace
  Download it via command line: $ sudo apt-get install grace
• qtgrace
  https://sourceforge.net/projects/qtgrace/
  It will run on Linux as well as on Windows and macOS.

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Further Reading

• https://bioinformaticsreview.com/20200807/tutorial-installing-autodock-vina-on-windows/
• https://bioinformaticsreview.com/20191226/mgl-tools-autodock-vina-installation-frequently-asked-questions-and-answers/
• https://bioinformaticsreview.com/20190618/video-tutorial-how-to-install-autodock-vina-on-ubuntu/
• https://bioinformaticsreview.com/20170729/how-to-install-autodock-vina-on-ubuntu/