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Tariq Abdullah

Tariq Abdullah has 16 articles published.

Algorithm and workflow of miRDB

in Algorithms/miRNA Target Prediction by

As mentioned in the previous article,¬†Micro RNAs (miRNAs) are the short endogenous RNAs (~22 nucleotides) and originate from the non-coding RNAs [1], produced in single-celled eukaryotes, viruses, plants, and animals [2]. They play significant roles in various biological processes such as degradation of mRNA [3]. Several databases exist storing a large amount of information about miRNAs, one of such databases miRBase [4] was explained in the previous article, today we will explain the algorithm of miRDB [5,6], another database for miRNA target prediction. Continue reading “Algorithm and workflow of miRDB” »

Web-based tools for protein-peptide docking

in Docking/Tools by

Protein-protein interactions are considered necessary in the interactome analysis as they play an important in various biological processes such as post-translational modifications and signal transduction, and short peptides mediate around 40% of protein-protein interactions[1]. They are also found involved in some kind of infections and critical human diseases such as cancer [2,3]. Continue reading “Web-based tools for protein-peptide docking” »

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” »

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