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...
Ahram Kim, Norbert Perrimon· Zenodo (CERN European Organi...· 0 citations
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...
J. T. Rodrigues, A. C. S. Batista, J. P. M. S. Lima et al.· Biophysical Reviews· 0 citations
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...
Xiang Chen, Pu Tian· bioRxiv· 0 citations
Reach audiences
Advertise in front of researchers, engineers, and readers.
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...
Yue He, Jacob S. Shine, S. Sriram et al.· Blood· 0 citations
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...
Significance Protein databases contain millions of rapidly accumulating sequences, while increasingly accurate 3D structure predictions provide unprecedented data for analysis. Predicted structures can also be encoded using a structure-focused alphabet alongside standard amino acid (AA) representations. We introduce a...
Divyanshu Shukla, Jonathan Martin, F. Morcos et al.· Proceedings of the National...· 0 citations
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...
Dania Camila Pulido Barrera, J. E. You, Angelo L. Angonezi et al.· Nature Structural & Molecula...· 0 citations
CropStabDB: a protein stability resource and Engineering Atlas of orthologue-supported substitutions for 30 plant proteomes Version 2.1.1. CropStabDB is a protein stability resource for 30 plant species - 29 crops and Arabidopsis thaliana, spanning 12 families and 1,425,716 proteins. Each protein carries a CropStab sco...
Chronic kidney disease (CKD) is a common acquired disorder in older cats and is associated with tubulointerstitial fibrosis, chronic inflammation, hypoxia, oxidative stress, and extracellular matrix (ECM) remodeling. Matrix metalloproteinase-7 (MMP7), a tubular epithelial-derived endopeptidase, has been implicated in r...
Sinan Vıcıl, Tuğrul Kırkulak· Journal of Advances in VetBi...· 0 citations
Background: Certain antiretroviral drugs, including efavirenz, have been associated with mitochondrial and oxidative effects in hepatic cells, but quantitative translation from nominal in vitro concentrations to an in vivo effect-site concentration remains uncertain. Methods: A hypothesis-generating physiologically bas...
Bárbara Costa, M. Gouveia, Nuno Vale· Pharmaceutics· 0 citations
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.
