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A short introduction to protein structures modification and ModFinder

in Sequence Analysis/Softwares/Tools by

A lot of protein structures are determined on a large scale and submitted in Protein Data Bank (PDB) www.rcsb.org [1]. After the experimental determination of these structures, they are used in many scientific studies and experiments are performed upon them such as mutagenesis, docking, and so on. Continue reading “A short introduction to protein structures modification and ModFinder” »

Alignment-free approaches for Sequence Analysis

in Algorithms/Sequence Analysis/Tools by

Multiple Sequence Alignment (MSA) is a fundamental aspect of Bioinformatics in order to identify the species, their functions, phylogeny, study the novel genes/ proteins, and so on. Multiple MSA tools are available with different specifications, which are based on the heuristic algorithm focusing on the speed rather than the accuracy. Continue reading “Alignment-free approaches for Sequence Analysis” »

How to perform docking in a specific binding site using AutoDock Vina?

in Featured/Tools by

AutoDock Vina is a bioinformatics tool which is used to perform in- silico docking of proteins with a ligand. It provides many options depending upon the needs of a user. This tool offers blind docking and binding in a specific pocket as well, which is sometimes more demanding when the binding site is already known. This article will guide you to dock a protein with a ligand in a specific binding site/ pocket. Continue reading “How to perform docking in a specific binding site using AutoDock Vina?” »

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