We have provided several tutorials on molecular dynamics (MD) simulation (please check further reading section). They include installation of simulation software, simulation of a simple protein,...
Cortex is a user-friendly framework for genome analysis [1]. It acquires less memory and is quite efficient in performance. It’s installation involves various steps. In this...
TREE-PUZZLE is a software to reconstruct phylogenetic trees using the maximum likelihood method [1,2]. It requires sequence data as input and implements a fast search algorithm...
Molecular dynamics (MD) simulation is one of the most widely used methods in bioinformatics. It needs high computation time and therefore, performed on workstations and servers....
genozip is a tool for lossless compression of large files including VCF, FASTQ, and SAM/BAM files [1]. In this article, we explain the usage of the...
Protein-protein interactions (PPIs) are essential to study to understand the molecular functions carried out by a group of proteins. Alcala et al., [1] developed a new...
Research is considered complicated. As it involves reading multiple research articles and reviews, devising hypotheses and appropriate experiments, and last but not the least, getting a...
GROMACS [1] is one of the most popular software in bioinformatics for molecular dynamic (MD) studies of macromolecules. We have provided different tutorials regarding MD simulation...
Researchers working in the field of bioinformatics are well-aware of the word “coordinates” in the context of docking. However, it could be a little difficult to...
Docking is performed in different ways depending upon the requirements. In some cases, it is required to dock a covalent ligand with the receptor. In this...
GROMOS96 is a well-known software package used for biomolecular simulations [1]. It can be used for the molecular dynamics simulation of protein, peptide, and protein-ligand complex...
In this article, a simple python script is provided that can be used to search for a specific character in a file.
MGLTools2 package comes with three different tools for docking: ADFR, AGFR, and AutoSite [1-3]. In this article, we will install this package on Ubuntu.
Flexible docking is when some residues in the interacting bodies (receptor and ligand) are kept flexible leaving the rest of the part rigid. In this article,...
Finding binding sites/pockets in a target protein is one of the important steps in docking studies. It is relatively easier to find a binding pocket in...
Bioinformatics is an interesting field of research combining biological sciences and computer sciences. In this article, we will discuss making careers in bioinformatics for starters.
DIAMOND is a program for high throughput pairwise alignment of DNA reads and protein sequences [1]. It is used for the high-performance analysis of large sequence...
In one of our previous articles, we have mentioned a few basic SQL queries to search in a database. In this article, we have described a...
In this article, basic SQL queries are described to create, update, drop, and perform other functions on a database.
FragGeneScan is a bioinformatics software to find fragmented genes in short reads [1]. It predicts genes by combining sequence models and codon usages in a hidden...
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