AI Networking Cookbook: Practical recipes for AI-assisted network automation and development
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1,870 papers
The symbiotic skin bacterium Staphylococcus epidermidis moisturizes human skin, contributes to protection against external pathogens, and supports innate immune stimulation. However, the interaction between collagen, a major skin protein, and S. epidermidis remains insufficiently explored. In this study, biofilm develo...
Lipoate is an essential protein-bound cofactor attached to conserved lysine residues in structurally related acceptor proteins, including GcvH of the glycine cleavage system and LbpA proteins required for sulfur oxidation by the sulfur-oxidizing heterodisulfide-like (sHdr) complex. The coexistence of distinct lipoylati...
Human milk (HM) is recommended for infants, as it provides essential nutrients and folded whey proteins, including lactoferrin (LF), that perform antimicrobial functions and aid in gut development. However, many rely on infant formulas (IFs), where there are no clear data on how much folded whey protein is present. W...
Data behind LIVIA Atlas: AlphaFold-Multimer protein interaction screens scored with iLIS (AFM-LIS), keeping the interface and contact residues of every prediction. livia-atlas-human-proteome.zip: human proteome-wide screen. Schmid et al. (2025), doi:10.1101/2025.11.10.687652. livia-atlas-human-kinase-tf.zip: human kina...
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Uric acid degradation is a model for understanding how gene duplication, loss, and functional divergence drive metabolic evolution. In hominoids and uricotelic animals, uric acid is the terminal purine catabolite, whereas most other taxa further degrade it to allantoin and beyond. Comparative genomics and structura...
This thesis uses X-ray crystallography and cryo-EM to show how structure dictates specificity in two unrelated systems: the lipid signalling enzyme Autotaxin and the transcriptional coregulator Zincore, from a single enzyme pocket to a multisubunit complex controlling gene expression. Part A: Autotaxin and lipid signal...
In a companion study, we introduced ProDive and used it to identify 318,289 high-confidence cross-family segment correspondences across all 25,545 Pfam families. Here we characterize the pervasiveness and biophysical context of the resulting mapped fragment resource. Graph-based community analysis shows that segment re...
Mechanisms of heme-iron (HI) absorption remain uncertain. Heme is probably absorbed by receptor-mediated endocytosis; iron is then enzymatically liberated from heme within endosomes, or in the cytosol. If heme is catabolized in endosomes, a transporter, such as DMT1, would be required to export ionic iron into the cyto...
The symbiotic skin bacterium Staphylococcus epidermidis moisturizes human skin, contributes to protection against external pathogens, and supports innate immune stimulation. However, the interaction between collagen, a major skin protein, and S. epidermidis remains insufficiently explored. In this study, biofilm develo...
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Proteins can be studied through their sequence statistics or structural properties. These represent complementary views that are useful but lack a quantitative framework to tell, family by family, which is most informative and how to combine them. We introduce a framework that builds both views in parallel: amino acid...
Chromosomes fold into distinct domains that regulate transcription, replication and repair. In addition to well-characterized topologically associating domains (TADs) and compartments, the diversity of heterochromatin domains remains poorly defined at the sequence level. Here, using single-molecule tracing of nascent h...
Proof of concept for watermarking AI-generated proteins while preserving biological function.
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
Scientists are using AlphaFold to strengthen a photosynthesis enzyme for resilient, heat-tolerant crops.
Explore how AlphaFold has accelerated science and fueled a global wave of biological discovery.
AlphaFold has revealed the structure of a key protein behind heart disease
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