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Where to find Docking and MD simulation software?

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Where to find Docking and simulation software?

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

Docking output analysis software

Simulation Software

MD Simulation plot visualization software


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/

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

Software

How to calculate binding pocket volume using PyVol plugin in PyMol?

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How to calculate binding pocket volume using PyVol plugin in PyMol?

Previously, we provided a tutorial for PyVol plugin [1] installation. In this article, we will calculate the binding pocket volume of protein using the same plugin in PyMol [2]. (more…)

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How to generate electron density map using Pymol?

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How to generate electron density map using Pymol?

Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.

(more…)

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Installing PyVOL plugin in Pymol on Ubuntu (Linux).

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Installing PyVOL plugin in Pymol on Ubuntu (Linux).

PyVOL [1] is an excellent plugin of Pymol [2] for pocket visualization of proteins. In this article, we will install the PyVOL plugin in Pymol on Ubuntu. (more…)

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