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MGL Tools & Autodock Vina installation: Frequently Asked Questions and Answers

in Softwares/Tips & Tricks/Tools by

I have been receiving several e-mails from researchers and students alike regarding the installation of MGL Tools and Autodock Vina on Ubuntu. Most questions are similar in nature, so I thought of answering them once and for all. In this article, I have collected some frequently asked questions and provided the link to their answers present in our question-answer section of Bioinformatics Review. Continue reading “MGL Tools & Autodock Vina installation: Frequently Asked Questions and Answers” »

Tutorial: Molecular dynamics (MD) simulation using Gromacs

in Molecular dynamics/Softwares/Tools by

Gromacs [1] is one of the most widely used software for molecular dynamics (MD) simulation of macromolecules. One of the previous articles, explains the installation of Gromacs on Ubuntu. This article is about the execution of Gromacs simulating a simple protein. This is a simple tutorial for MD simulation of a protein. Continue reading “Tutorial: Molecular dynamics (MD) simulation using Gromacs” »

Installing and executing ProtTest3 on Ubuntu

in Phylogenetics/Softwares/Tools by

Prottest3 is a software which is used to select a best-fit amino acid replacement model for a set of protein sequences [1]. ProtTest3 finds a best-fit model on the basis of the smallest value of one of three criterions: Akaike Information Criterion (AIC), Corrected Akaike Information Criterion, Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT) selected by the user. In this article, we will learn how to download and install the command-line version of ProtTest3 on Ubuntu. Continue reading “Installing and executing ProtTest3 on Ubuntu” »

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