Software
GENPPI- Tool to create protein interaction networks from genomes.
A new software called GENPPI [1] is developed to create protein interaction networks from genomes.
GENPPI creates networks of interactions based on three characteristics: conserved gene neighborhoods, phylogenetic profiles, and gene fusions. This software predicts correct evolutionary relationships among species as evident from the average nucleotide identity analyses performed by the authors [1].
The working of GENPPI is based on HistoFasta Heuristic algorithm. As compared to STRING, GENPPI provides more accurate results [1]. Authors tested GENPPI on 50 genomes. It created protein interaction networks with an average size of 2200 genes in less than 40 min on a conventional computer.
GENPPI is a platform independent software written in Common Lisp without any further requirements. It is available to download at genppi.facom.ufu.br and on GitHub (https://github.com/santosardr/genppi) as well.
For more information, read here.
References
- Anjos, W.F., Lanes, G.C., Azevedo, V.A. et al. (2021). GENPPI: standalone software for creating protein interaction networks from genomes. BMC Bioinformatics 22, 596.
Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.
PyVOL [1] is an excellent plugin of Pymol [2] for pocket visualization of proteins. In this article, we will install the PyVOL plugin in Pymol on Ubuntu. (more…)
You must be logged in to post a comment Login