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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 execute matlab from terminal in Ubuntu (Linux)?

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How to execute matlab from terminal in Ubuntu (Linux)?

While trying to install Matlab [1], it generally gives an error stating “matlab: command not found.”. Here, we provide a solution to this error.

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Software

How to install Kpax on Ubuntu (Linux)?

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How to install Kpax on Ubuntu (Linux)?

Kpax is a bioinformatics program to search and align protein structures [1]. It is currently available for Linux platforms only. In this article, we are going to install the latest version of Kpax (5.1.3) on Ubuntu (Linux). (more…)

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Secondary structure

How to run do_dssp command (mkdssp) in Gromacs 2022?

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How to run do_dssp command in Gromacs 2022?

In the latest version of GROMACS (2022) [1], there are some issues regarding the gmx do_dssp command. Apparently, this command either does not run displaying a fatal error, or if it runs then it does not read any frame from MD simulation files. In this article, we are going to run the same command for GROMACS 2022. (more…)

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