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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 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” »

Benchmark databases for multiple sequence alignment: An overview

in Algorithms/Sequence Analysis/Softwares by

Multiple sequence alignment (MSA) is a very crucial step in most of the molecular analyses and evolutionary studies. Many MSA programs have been developed so far based on different approaches which attempt to provide optimal alignment with high accuracy. Basic algorithms employed to develop MSA programs include progressive algorithm [1], iterative-based [2], and consistency-based algorithm [3]. Some of the programs incorporate several other methods into the process of creating an optimal alignment such as M-COFFEE [4] and PCMA [5]. Continue reading “Benchmark databases for multiple sequence alignment: An overview” »

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