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” »
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?” »
Multiple sequence alignments (MSAs) are quite valuable in terms of studying new enzymes or organisms. They provide insights to identify their structures and functions. For this purpose, we need sophisticated tools to analyze large MSAs. This article will mention a few important and useful alignment viewers with various functions to perform on the MSAs. Continue reading “Most widely used tools to analyze multiple sequence alignments” »