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

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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 blast against a particular set of local sequences (local database)?

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BLAST [1,2] is a local alignment tool widely used as a preliminary step for the identification of gene or protein functions. The command-line package of NCBI-Blast offers several useful features. These features include making a BLAST database of a set of nucleotide or protein sequences, blast a query sequence against them or all-against-all blast. In this article, these commands are explained.  Continue reading “How to blast against a particular set of local sequences (local database)?” »

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

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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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