A first theme concerns the design of green catalytic systems that improve the physicochemical properties of high-value bioactive compounds. The contribution by the group exemplifies this direction through the whole-cell-catalyzed cinnamoylation of phillyrin (Yang et al., 2026). By combining Aspergillus oryzae whole cel...
Xiang Zhou, Hongzhen Luo, Jun Liu et al.· Frontiers in Microbiology· 0 citations
Soritesidine (SOR) is a potent proteinaceous toxin from the marine sponge Spongosorites sp. that is toxic to mammalian cells, brine shrimp larvae, sea hare embryos, and mice. Although SOR exhibits divalent metal ion-dependent DNase activity, its molecular identity and mechanism of action remained unknown. We determined...
Hiromi Watari, Koji Nakano, M. Kitano et al.· Toxins· 0 citations
This software provides a Python-based platform for transforming time-resolved experimental data into sound. Initially developed to explore protein-folding dynamics measured using single-molecule optical tweezers, the algorithm is designed to be applicable to a broad range of one-dimensional experimental trajectories an...
Banin Raffaello, Qiuyan Li· Zenodo (CERN European Organi...· 0 citations
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Neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and related proteinopathies are characterized by the misfolding, aggregation, and accumulation of specific proteins that disrupt neuronal homeostasis, leading to neuronal death. Despite major adva...
Arunabh Choudhury, Sneh Prabha, Mohammad Umar Saeed et al.· Figshare· 0 citations
The crosstalk between the liver and the lung is complex and not yet fully understood; however, recent studies suggest that metabolic dysfunction, often originating in the liver, can influence lung injury and other lung diseases. The current study investigates the role of bile acids (BA) in mediating lung injury in a mo...
Ahmad Salhab, Johnny Amer, Rifaat Safadi· International Journal of Mol...· 0 citations
A full characterisation of a molecular system requires its metastable states, their populations and their interconversion rates. Molecular Dynamics can in principle provide this characterisation but is limited by sampling and by force-field inaccuracies. Enhanced sampling addresses the first problem, but typically requ...
Z. Faidon Brotzakis, Νικόλαος Ρεκατσίνας· bioRxiv (Cold Spring Harbor...· 0 citations
Triple-negative breast cancer (TNBC) is an aggressive and molecularly heterogeneous breast cancer subtype. We developed a six-gene oxidative stress-related signature (BAG5, ANXA2, LONP1, GBE1, CBR1, and DDIT4) in GSE58812 (107 patients; 29 deaths) and evaluated its transportability in GSE21653 (83 TNBC patients; 25 dis...
Sirinya Sitthirak, Nopparut Gota, Jie Cui et al.· Oxygen· 0 citations
Accumulation of aberrant and unfolded proteins induce cellular stresses and contributes in human to diseases and aging. Several cellular pathways combat the formation of these deleterious molecules. Recently, processes limiting the production of unwanted polypeptides through the co-translational degradation of their me...
G. Caulier, F. Mauxion, B. Séraphin· bioRxiv· 0 citations
Code and per-dataset results for the second revision of manuscript BIOINF-2026-2348 (Bioinformatics). This version adds: (1) the unified-protocol pooling contrast between the random and leakage-free splits with per-dataset paired bootstrap statistics; (2) published ProteinGym v1.3 anchors recomputed per assay on the sa...
Yutao Guo, Zihan Zhang, Xuezhou Zhao et al.· Zenodo (CERN European Organi...· 0 citations
Membrane contact sites (MCS) are regions in the cell where the membranes of two organelles come into close proximity without fusing. Contact sites between mitochondria and the endoplasmic reticulum (MERCs) are arguably the most well-studied MCS. The study of MERCs is commonly conducted using fluorescence colocalization...
Code accompanying the paper "Ancient amino acid sets enable stable protein folds" (Giacobelli, Andersson, et al., bioRxiv 2025, doi:10.1101/2025.10.29.685319). Contents: Protein design pipeline: RFdiffusion backbones, ProteinMPNN sequences restricted to a 10-amino-acid ancient alphabet, and a 20-amino-acid comparison d...
Sebastian Andersson, Tereza Neuwirthová· Zenodo (CERN European Organi...· 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.
