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Where to find Docking and MD simulation software?

Dr. Muniba Faiza
Last updated: June 4, 2021 6:40 pm
Dr. Muniba Faiza
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Where to find Docking and simulation software?
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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.

Contents
Docking softwareDocking output analysis softwareSimulation SoftwareMD Simulation plot visualization softwareFurther Reading

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    https://www.gromacs.org/Downloads_of_outdated_releases (For outdated releases)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.

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/
TAGGED:dockingdocking softwaredocking toolsmd simulationsimulation tools
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ByDr. Muniba Faiza
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Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba
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