AIMC Topic: Viral Proteins

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Empathi: embedding-based phage protein annotation tool by hierarchical assignment.

Nature communications
Bacteriophages, viruses infecting bacteria, are estimated to outnumber their cellular hosts by 10-fold, acting as key players in all microbial ecosystems. Under evolutionary pressure by their host, they evolve rapidly and encode a large diversity of ...

A graph neural network-based approach for predicting SARS-CoV-2-human protein interactions from multiview data.

PloS one
The COVID-19 pandemic has demanded urgent and accelerated action toward developing effective therapeutic strategies. Drug repurposing models (in silico) are in high demand and require accurate and reliable molecular interaction data. While experiment...

Computational function prediction of bacteria and phage proteins.

Microbiology and molecular biology reviews : MMBR
SUMMARYUnderstanding protein functions is crucial for interpreting microbial life; however, reliable function annotation remains a major challenge in computational biology. Despite significant advances in bioinformatics methods, ~30% of all bacterial...

In-silico evaluation of Azadirachta indica-derived Daucosterol against key viral proteins of Ebolavirus using ML and MD simulations approach.

Journal of biological physics
Ebola virus disease (EVD) is an acute life-threatening disease caused by highly pathogenic Ebolavirus (EBOV), with reported case fatality rates reaching 90%. There have been numerous EBOV outbreaks and epidemics since the first outbreak was reported ...

A systematic evaluation of the language-of-viral-escape model using multiple machine learning frameworks.

Journal of the Royal Society, Interface
Predicting the evolutionary patterns of emerging and endemic viruses is key for mitigating their spread. In particular, it is critical to rapidly identify mutations with the potential for immune escape or increased disease burden. Knowing which circu...

Machine learning assessment of zoonotic potential in avian influenza viruses using PB2 segment.

BMC genomics
BACKGROUND: Influenza A virus (IAV) is a major global health threat, causing seasonal epidemics and occasional pandemics. Particularly, Influenza A viruses from avian species pose significant zoonotic threats, with PB2 adaptation serving as a critica...

Genome evolution of Kaposi sarcoma-associated herpesvirus (KSHV).

Journal of virology
UNLABELLED: Kaposi sarcoma (KS) is the most common cancer in people living with HIV (PLWH), particularly in sub-Saharan Africa (SSA), where Kaposi sarcoma herpesvirus (KSHV or human herpesvirus 8 [HHV-8]) is endemic. In KSHV endemic areas, the overal...

Prediction and Evaluation of Coronavirus and Human Protein-Protein Interactions Integrating Five Different Computational Methods.

Proteins
The high lethality and infectiousness of coronaviruses, particularly SARS-Cov-2, pose a significant threat to human society. Understanding coronaviruses, especially the interactions between these viruses and humans, is crucial for mitigating the coro...

Deep Learning-Based Comparative Prediction and Functional Analysis of Intrinsically Disordered Regions in SARS-CoV-2.

International journal of molecular sciences
This study explores the role of intrinsically disordered regions (IDRs) in the SARS-CoV-2 proteome and their potential as targets for small-molecule drug discovery. Experimentally validated intrinsic disordered regions from the literature were utiliz...

Cucumber green mottle mosaic virus encodes additional small proteins with specific subcellular localizations and virulence function.

Science China. Life sciences
The vast majority of known viruses belong to the positive-sense single-stranded RNA (+ssRNA) class. Tobamoviruses are among the most destructive plant viruses and threaten global food security. It is generally accepted that +ssRNA viruses including t...