LigPlot+ is a bioinformatics software to visually analyze the protein-ligand interactions in 2D [1]. It requires a Java interface to run and can be executed on...
DeepView (Swiss-PDB Viewer) [1] is used to analyze multiple proteins simultaneously. Protein structure alignment, active site comparison, amino acid mutations, H-bonds, and other relevant functions can...
I have received several e-mails from researchers and students alike regarding installing MGL Tools and Autodock Vina on Ubuntu. Most questions are similar in nature, so...
Gromacs [1] is one of the most widely used software for molecular dynamics (MD) simulation of macromolecules. One of the previous articles, explains the installation of...
Prottest3 is a software which is used to select a best-fit amino acid replacement model for a set of protein sequences [1]. ProtTest3 finds a best-fit...
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...
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...
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...
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...
MODELLER is a software package that is used to predict protein three-dimensional structures [1,2]. MODELLER can be used for other tasks such as modeling of loops...
This is a video tutorial of Autodock Vina installation on Ubuntu, based on our existing tutorial.
Blind docking is done when the catalytic/binding residues are unknown in a protein, hence, the binding pocket is unknown. In a previous article, we showed how to...
If you want to get a quick idea about the non-synonymous vs synonymous (dN/dS) substitutions, you can easily use MEGA software [1]. Although HYPHY/Datamonkey provides the...
In the last article on Bioinformatics Review, the utilization of Roary [1] and Prokka [2] was explained to create a pangenome from isolated genome sequences. This...
Roary is a pangenome genome pipeline, which calculates pangenome of a set of related prokaryotic isolates [1]. It takes annotated assemblies in the gff3 format generated...
Structure modeling of chemical compounds finds essential application in the field of cheminformatics. It is used to study the structural stability, metal-ion bonding, the presence of...
Stem cells are cells that can be differentiated into other types and are thus pluripotent with the ability to become cells of all lineages. Cells found...
Protein-protein interactions are considered necessary in interactome analysis as they play an important in various biological processes such as post-translational modifications and signal transduction, and short...
This is a video added to our existing tutorial
Most of the times, it is a very tedious job to convert file formats in bioinformatics, especially when we are dealing with phylogeny. Most of the...
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