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Author

Tariq Abdullah

Tariq Abdullah has 28 articles published.

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” »

How to cluster peptide/protein sequences using cd-hit software?

in Softwares/Tools by

Cd-hit is one of the most widely used programs to cluster biological sequences [1]. It helps in removing the redundant sequences and provides better results in the sequence analyses. Cd-hit is used for sequence-based clustering by making clusters of a particular cut off provided as an input. It uses a single linkage clustering and finds a representative sequence for each cluster. In this article, we will learn how to cluster a set of protein sequences using cd-hit software. Continue reading “How to cluster peptide/protein sequences using cd-hit software?” »

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