Accurately identifying genes responsible for specific functions is a cornerstone of biological research, but current methods are often limited to single-species analyses. Here, we present a novel method, called Genomic and Phenotype-based machine lea...
Toxin-antitoxin (TA) systems are widespread antiphage defense elements in bacteria that may impede successful phage therapy. Phage-encoded inhibitors of these systems have been discovered that enhance phage infection capacity. We used fragment-based ...
Extended-spectrum β-lactamases in Escherichia coli poses a significant threat for clinicians in tertiary healthcare settings, rendering treatments ineffective with newer β-lactam-β-lactamase inhibitors combinations. To overcome this, the present stud...
Journal of chemical theory and computation
Sep 2, 2025
Sodium-proton antiporter NhaA of is a paradigm to investigate the mechanistic basis of the fundamental Na/H exchange in cells. However, all existing crystal structures of NhaA are inward-facing (IF), and the putative outward-facing (OF) structures a...
Iron is an essential nutrient for most bacteria and is often growth-limiting during infection, due to the host sequestering free iron as part of the innate immune response. To obtain the iron required for growth, many bacterial pathogens encode trans...
The DNA binding of most Escherichia coli Transcription Factors (TFs) has not been comprehensively mapped, and few have models that can quantitatively predict binding affinity. We report the global mapping of in vivo DNA binding for 139 E. coli TFs us...
Journal of chemical theory and computation
Apr 10, 2025
This work introduces LEGOLAS, a fully open source TorchANI-based neural network model designed to predict NMR chemical shifts for protein backbone atoms (N, Cα, Cβ, C', HN, Hα). LEGOLAS has been designed to be fast without loss of accuracy, as our mo...
The first step in bottom-up proteomics is the assignment of measured fragmentation mass spectra to peptide sequences, also known as peptide spectrum matches. In recent years novel algorithms have pushed the assignment to new heights; unfortunately, d...
Escherichia coli (E. coli), a gram-negative bacterium, quickly colonizes in the human gastrointestinal tract after birth and typically sustains a long-term, symbiotic relationship with the host. However, certain virulent strains of E. coli can cause ...
Protein solubility is a critical parameter that determines the stability, activity, and functionality of proteins, with broad and far-reaching implications in biotechnology and biochemistry. Accurate prediction and control of protein solubility are e...
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