Bacteriophage Bioinformatics 2.0

Dear Colleagues,

The rise of antibiotic resistance to critical levels and the simultaneous increasing number of bacterial pathogens point to the urgent need to produce new medications. While alternative antimicrobial agents were discovered nearly a century ago, the first of which were identified as bacteriophages, they have not been analysed or used to any great extent. At that time, researchers possessed neither the proper equipment nor the possibility to perform high-throughput screening (HTS) of protein/ligand interactions, nor quantitative methods of comparative analysis, which provide information about these agents as well as their activity and specificity. Nowadays, this has radically changed, as structural, biochemical, and computational methods have emerged that complement each other. A new impact was done in the last few year by usage deep learning methods for analysis and prediction of protein–protein interactions (PPI) that are essential for revelation of interactions bacteriophages/host cell. This type of studies are essential for understanding and design of novel drugs and phages with specific properties. Hybrid approaches based on the combination of structural methods and bioinformatics for the analysis of sequence databases, interactions of ligands/proteins, and computational statistics, with high-throughput biochemical methods revealing significant information on phage–pathogen interactions, their function, and their dependence on animal or human host environments. Moreover, phage therapy has become a more broadly used treatment method. However, even these successful efforts require improvements regarding the analysis and comparison of the components of bacteriophages and their interactions with pathogenic hosts, as well as the revelation of their active sites, specificity (interactions with receptors), and the principles of the regulation of their activity. In this context, hybrid approaches, which include bioinformatics and structural, biochemical, and microbiological studies, play an important role in the development of new medications.

This Special Issue of Viruses highlights innovations in hybrid methods of analysis and the search for effective, even modified, synthetic phages via combined biochemical, structural, and bioinformatic methods, and demonstrates the results achieved by the implementation and combination of innovative ideas. These approaches can be used in the identification of specific phages or in the creation of synthetic phages (or pseudo-phage particles) that, through the analysis of their properties, can be applied to the field of phage therapy or in the food industry.

This Special Issue includes the following:

1. Reviews describing the available tools for the analysis of phage genomes or comparative assessments of different packages;
2. How predictions of specific types of bacteriophages (virulent or temperate) can be made through using the computational analysis of phage genomes;
3. The classification of phages based on their genome sequences;
4. The applications of bioinformatics in the verification and classification of phage proteins;
5. The optimisation of high-throughput experimental methods in the analysis of phages, utilising bioinformatic approaches;
6. Methods of phage–bacterium interaction analysis and links to their life state (virulent or temperate);
7. The application of deep learning methods to analysis of phage/cell interactions
8. The goals, designs, and applications of synthetic phages in the pharmaceutic and food industries.

Prof. Dr. Elena Orlova
Guest Editor

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• viruses
• bacteriophage
• bacteriophage classification
• genome
• bioinformatics
• deep learning
• computational tools
• structural organisation
• infectivity
• function
• structural methods
• electron microscopy
• X-ray
• NMR
• high-throughput screening

• Bacteriophage Bioinformatics in Viruses (9 articles)