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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” »

Sequence search against a set of local sequences (local database) using phmmer

in Proteomics/Sequence Analysis/Softwares by

PHMMER is a sequence analysis tool used for protein sequences (http://hmmer.org; version 3.1 b2). It is available online as a web server and as well as a part of the HMMER stand-alone package (http://hmmer.org; version 3.1 b2). HMMER offers various useful features such as multiple sequence alignment including the file format conversion.  Continue reading “Sequence search against a set of local sequences (local database) using phmmer” »

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