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Tariq Abdullah

Tariq Abdullah has 29 articles published.

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” »

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” »

Autodock VinaXB for molecular docking of protein complexes containing halogen bonding interactions

in Docking/Softwares/Tools by

Molecular docking is the most widely used technique which is used to predict the binding affinities and bound conformations of a ligand and protein complex. Autodock Vina [1] is one of the most widely used docking software for structure-based drug designing.  Continue reading “Autodock VinaXB for molecular docking of protein complexes containing halogen bonding interactions” »

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