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A new high-level Python interface for MD simulation using GROMACS

in Algorithms/Bioinformatics News/Molecular dynamics/Softwares/Tools by

The roots of the molecular simulation application can be traced back to physics where it was applied to simplified hard-sphere systems [1]. This field of molecular simulation study has gained a lot of interest since then and applied to perform simulations to fold small protein at multi-microsecond scale [2-4], predict functional properties of receptors and to capture the intermediate transitions of the complex [5], and to study the movement and behavior of ligand in a binding pocket and also to predict interactions between receptors and ligands [6,7]. Continue reading “A new high-level Python interface for MD simulation using GROMACS” »

Simulated sequence alignment software: An alternative to MSA benchmarks

in Algorithms/Databases/Sequence Analysis/Softwares/Tools by

In our previous article, we discussed different multiple sequence alignment (MSA) benchmarks to compare and assess the available MSA programs. However, since the last decade, several sequence simulation software have been introduced and are gaining more interest. In this article, we will be discussing various sequence simulating software being used as alternatives to MSA benchmarks. Continue reading “Simulated sequence alignment software: An alternative to MSA benchmarks” »

How to perform protein structure modeling using I-Tasser stand-alone tool?

in Softwares/Structural Bioinformatics/Structure Prediction/Tools by

I-Tasser stands for the iterative threading assembly refinement is a well-known tool for ab-initio structure modeling of proteins [1]. It uses secondary-structure enhanced profile-profile threading alignment (PPA) [2] and iterative structure assembly simulations using a threading assembly refinement program [3]. I-Tasser is used for ab-initio prediction when the similarity of a protein is quite low (<=30%). Mostly, the I-Tasser server [4] is used for this purpose, which can be easily accessed by registering with a valid institutional mail ID.  In this article, we will learn how to predict a protein structure using the I-Tasser standalone version. Continue reading “How to perform protein structure modeling using I-Tasser stand-alone tool?” »

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