Related papers: PhaGO: Protein function annotation for bacteriopha…
Filamentous phage, such as fd used in this study, are thread-shaped bacterial viruses. Their outer coat is a tube formed by thousands equal copies of the major coat protein pVIII. We constructed libraries of random peptides fused to all…
Designing novel proteins with desired characteristics remains a significant challenge due to the large sequence space and the complexity of sequence-function relationships. Efficient exploration of this space to identify sequences that meet…
Background: Protein-protein interaction (PPI) network analyses are highly valuable in deciphering and understanding the intricate organisation of cellular functions. Nevertheless, the majority of available protein-protein interaction…
\textbf{Introduction:} Accurate prediction of Phage Virion Proteins (PVP) is essential for genomic studies due to their crucial role as structural elements in bacteriophages. Computational tools, particularly machine learning, have emerged…
Pathogen-mediated competition, through which an invasive species carrying and transmitting a pathogen can be a superior competitor to a more vulnerable resident species, is one of the principle driving forces influencing biodiversity in…
The terminase motors of bacteriophages have been shown to be among the strongest active machines in the biomolecular world, being able to package several tens of kilobase pairs of viral genome into a capsid within minutes. Yet these motors…
Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data…
Rapid advancements in collection and dissemination of multi-platform molecular and genomics data has resulted in enormous opportunities to aggregate such data in order to understand, prevent, and treat human diseases. While significant…
Protein function is driven by cohesive substructures, such as catalytic triads, binding pockets, and structural motifs, that occupy only a small fraction of a protein's residues. Yet existing pipelines built on protein encoders do not model…
With the development of next generation sequencing techniques, it is fast and cheap to determine protein sequences but relatively slow and expensive to extract useful information from protein sequences because of limitations of traditional…
The capability of accurate prediction of protein functions and properties is essential in the biotechnology industry, e.g. drug development and artificial protein synthesis, etc. The main challenges of protein function prediction are the…
Segmentation and genome annotation (SAGA) algorithms are widely used to understand genome activity and gene regulation. These algorithms take as input epigenomic datasets, such as chromatin immunoprecipitation-sequencing (ChIP-seq)…
Identifying novel functional protein structures is at the heart of molecular engineering and molecular biology, requiring an often computationally exhaustive search. We introduce the use of a Deep Convolutional Generative Adversarial…
Bacteriophage viruses, one of the most abundant entities in our planet, lack the ability to move independently. Instead, they crowd fluid environments in anticipation of a random encounter with a bacterium. Once they land on the cell body…
Proteins carry out biological functions through the coordinated action of groups of residues organized into structural arrangements. These arrangements, which we refer to as protein units, exist at an intermediate scale, being larger than…
Bacteriophages are viruses infecting bacteria and archaea. Many phage species cause infections which lead to the certain death of the infected prokaryotic host cell and the release of a large batch of phage progeny, yet they have been able…
Motivation: In the last few years a growing interest in biology has been shifting towards the problem of optimal information extraction from the huge amount of data generated via large scale and high-throughput techniques. One of the most…
Accurate prediction of virus-host interactions is critical for understanding viral ecology and developing applications like phage therapy. However, the growing number of computational tools has created a complex landscape, making direct…
Genome annotation is essential for understanding the functional elements within genomes. While automated methods are indispensable for processing large-scale genomic data, they often face challenges in accurately predicting gene structures…
Automatic protein function prediction (AFP) is classified as a large-scale multi-label classification problem aimed at automating protein enrichment analysis to eliminate the current reliance on labor-intensive wet-lab methods. Currently,…