BACKGROUND: Staphylococcus aureus and Staphylococcus epidermidis are tenacious pathogens that cause toxic shock syndrome. Accessory gene regulator (Agr) of Staphylococcus sp. controls the expression of multiple genes that encode virulence properties....
CRISPR-Cas systems revolutionize life science. Metagenomes contain millions of unknown Cas proteins. Traditional mining relies on protein sequence alignments. In this work, we employ an evolutionary scale language model (ESM) to learn the information...
Bacteria are constantly exposed to diverse environmental stresses, necessitating complex adaptive mechanisms for survival. Thermus thermophilus, a thermophilic extremophile, serves as an excellent model for investigating these responses due to its re...
Microbiology and molecular biology reviews : MMBR
Aug 18, 2025
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...
Metabolomics : Official journal of the Metabolomic Society
Aug 12, 2025
INTRODUCTION: The degree of antimicrobial resistance demonstrated by carbapenemase-producing Enterobacterales (CPE) represents a growing public health challenge. Conventional methods for detecting CPE involve culture-based techniques with lengthy inc...
International journal of biological macromolecules
Jul 23, 2025
Targeting distal mutations holds promising implications for enzyme engineering. Here, we present an open-source computational workflow designed to explore the functional impact of distal sites, demonstrated on an artificial enzyme built on the widely...
The emergence of Carbapenem-resistant (CRKP) represents a major public health concern, primarily driven by its ability to evade a wide range of antibiotics. Despite extensive genomic studies, proteomic insights into antibiotic resistance mechanisms ...
The detection of mixed-species bacterial samples plays a vital role in ensuring food safety, yet research in this area remains notably limited. This study investigates the integration of MALDI-TOF MS-derived peptidome profiles with artificial intelli...
Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we r...
Bio-instructive materials that intrinsically inhibit biofilm formation have significant anti-biofouling potential in industrial and healthcare settings. Since bacterial surface attachment is sensitive to surface topography, we experimentally surveyed...
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