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Author

Tariq Abdullah

Tariq Abdullah has 14 articles published.

A new high-level Python interface for MD simulation using GROMACS

in Algorithms/Bioinformatics News/Molecular dynamics/Softwares/Tools by

The roots of the molecular simulation application can be traced back to physics where it was applied to simplified hard-sphere systems [1]. This field of molecular simulation study has gained a lot of interest since then and applied to perform simulations to fold small protein at multi-microsecond scale [2-4], predict functional properties of receptors and to capture the intermediate transitions of the complex [5], and to study the movement and behavior of ligand in a binding pocket and also to predict interactions between receptors and ligands [6,7]. Continue reading “A new high-level Python interface for MD simulation using GROMACS” »

How to execute Unix/shell commands in a Perl script?

in Bioinformatics Programming by

BioPerl is a collection of Perl modules which is used to write Perl scripts applied in bioinformatics [1]. It is used in bioinformatics programmings such as in developing source codes, standalone software/tools, and algorithms. It’s easy to install and provide various modules which make it easier to execute different functions. However, Python is mostly preferred over the Perl language, still, some of the bioinformatics software is based on Perl such as the standalone version of I-TASSER. Sometimes, it’s big trouble to execute some Unix/shell commands in Perl script for the beginners, it’s difficult to decide which function would be specific to a condition. Therefore, this article is a guide for the execution of Unix/shell commands in Perl script. Continue reading “How to execute Unix/shell commands in a Perl script?” »

How to perform protein structure modeling using I-Tasser stand-alone tool?

in Softwares/Structural Bioinformatics/Structure Prediction/Tools by

I-Tasser stands for the iterative threading assembly refinement is a well-known tool for ab-initio structure modeling of proteins [1]. It uses secondary-structure enhanced profile-profile threading alignment (PPA) [2] and iterative structure assembly simulations using threading assembly refinement program [3]. I-Tasser is used for ab-initio prediction when the similarity of a protein is quite low (<=30%). Mostly, the I-Tasser server [4] is used for this purpose, which can be easily accessed by registering with a valid institutional mail ID.  In this article, we will learn how to predict a protein structure using I-Tasser standalone version. Continue reading “How to perform protein structure modeling using I-Tasser stand-alone tool?” »

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